Nothing
R/normalize.R
In limmaGUI: GUI for limma Package With Two Color Microarrays
Defines functions
GetBetweenArrayNormalizationMethod
WithinBetweenOrBoth
ExportAvalues
ExportMvalues
AboutNormalization
NormalizeNow
GetWithinArrayNormalizationMethod
Documented in
AboutNormalization
ExportAvalues
ExportMvalues
GetBetweenArrayNormalizationMethod
GetWithinArrayNormalizationMethod
NormalizeNow
WithinBetweenOrBoth
GetWithinArrayNormalizationMethod <- function()
{
Try(ttGetWithinArrayNormalizationMethod<-tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttGetWithinArrayNormalizationMethod,"Within-Array Normalization Method"))
Try(tkwm.deiconify(ttGetWithinArrayNormalizationMethod))
Try(tkgrab.set(ttGetWithinArrayNormalizationMethod))
Try(tkframe1 <- tkframe(ttGetWithinArrayNormalizationMethod,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a method for within-array normalization.",font=.limmaGUIglobals$limmaGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(methnorm <- tclVar(WithinArrayNormalizationMethod))
# Try(none.but <- tkradiobutton(tkframe2,text="None",variable=methnorm,value="none",font=.limmaGUIglobals$limmaGUIfont2))
Try(median.but <- tkradiobutton(tkframe2,text="Median",variable=methnorm,value="median",font=.limmaGUIglobals$limmaGUIfont2))
Try(global.but <- tkradiobutton(tkframe2,text="Global loess",variable=methnorm,value="loess",font=.limmaGUIglobals$limmaGUIfont2))
Try(printtip.but <- tkradiobutton(tkframe2,text="Print-tip group loess",variable=methnorm,value="printtiploess",font=.limmaGUIglobals$limmaGUIfont2))
Try(composite.but <- tkradiobutton(tkframe2,text="Composite",variable=methnorm,value="composite",font=.limmaGUIglobals$limmaGUIfont2))
Try(robustspline.but <- tkradiobutton(tkframe2,text="Robust Spline",variable=methnorm,value="robustspline",font=.limmaGUIglobals$limmaGUIfont2))
# Try(tkgrid(none.but,column=2))
Try(tkgrid(median.but,column=2))
Try(tkgrid(global.but,column=2))
Try(tkgrid(printtip.but,column=2))
Try(tkgrid(composite.but,column=2))
Try(tkgrid(robustspline.but,column=2))
# Try(tkgrid.configure(none.but,median.but,global.but,printtip.but,composite.but,robustspline.but,sticky="w"))
Try(tkgrid.configure(median.but,global.but,printtip.but,composite.but,robustspline.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(NewNormalizationMethod <- "")
onOK <- function()
{
Try(NewNormalizationMethod<<-tclvalue(methnorm));
Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));
Try(tkdestroy(ttGetWithinArrayNormalizationMethod))
Try(if (NewNormalizationMethod==WithinArrayNormalizationMethod)
return())
Try(WithinArrayNormalizationMethod <- NewNormalizationMethod)
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(MA.Available$WithinArrays <- FALSE)
Try(MA.Available$Both <- FALSE)
Try(MA.Available$BetweenArrays <- FALSE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinOnly","WithinOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));Try(tkdestroy(ttGetWithinArrayNormalizationMethod));NewNormalizationMethod<-"";Try(tkfocus(.limmaGUIglobals$ttMain))},font=.limmaGUIglobals$limmaGUIfont2))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(help("normalizeWithinArrays",help_type="html")),font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetWithinArrayNormalizationMethod, "<Return>",onOK))
Try(tkbind(ttGetWithinArrayNormalizationMethod, "<Destroy>", function() {Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttGetWithinArrayNormalizationMethod))
Try(tkdestroy(ttGetWithinArrayNormalizationMethod))
# This return value below is not used. The function above is used for its effect
# on WithinArrayNormalizationMethod in limmaGUIenvironment
return(NewNormalizationMethod)
}
NormalizeNow <- function()
{
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(ArraysLoaded <- get("ArraysLoaded", envir=limmaGUIenvironment))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
if (ArraysLoaded==FALSE)
{
Try(tkmessageBox(title="Normalization",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.limmaGUIglobals$ttMain))
return()
}
if (NormalizedMADataWasImported==TRUE)
{
Try(tkmessageBox(title="Normalization",message="Normalized data was imported. Impossible to recover raw data to renormalize.",type="ok",icon="error"))
Try(tkfocus(.limmaGUIglobals$ttMain))
return()
}
Try(RG <- get("RG",envir=limmaGUIenvironment))
Try(SetLayoutParamReturnVal <- 1)
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(if (length(maLayout)==0) SetLayoutParamReturnVal <-Try(SetLayoutParameters()))
Try(if (SetLayoutParamReturnVal==0) return())
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(NormalizeWithinArraysMB <-tkmessageBox(title="Normalization Within Arrays",message="Normalize Within Arrays?",type="yesnocancel",icon="question",default="yes"))
Try(WhetherToNormalizeWithinArrays <- tclvalue(NormalizeWithinArraysMB))
if (WhetherToNormalizeWithinArrays=="cancel")
return()
Try(if (WhetherToNormalizeWithinArrays=="yes")
{
Try(GetWithinArrayNormMethodVal<- GetWithinArrayNormalizationMethod())
Try(if (GetWithinArrayNormMethodVal=="") return())
})
Try(NormalizeBetweenArraysMB <-tkmessageBox(title="Normalization Between Arrays",message="Normalize Between Arrays?",type="yesnocancel",icon="question",default="no"))
Try(WhetherToNormalizeBetweenArrays <- tclvalue(NormalizeBetweenArraysMB))
if (WhetherToNormalizeBetweenArrays=="cancel")
return()
Try(if (WhetherToNormalizeBetweenArrays=="yes")
{
Try(GetBetweenArrayNormMethodVal<- GetBetweenArrayNormalizationMethod())
Try(if (GetBetweenArrayNormMethodVal=="") return())
})
Try(tkconfigure(.limmaGUIglobals$ttMain,cursor="watch"))
Try(tkfocus(.limmaGUIglobals$ttMain))
Try(WeightingType <- get("WeightingType",envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(if (!exists("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(BetweenArrayNormalizationMethod <- "scale")
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
})
Try(BetweenArrayNormalizationMethod <- get("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
if (WhetherToNormalizeWithinArrays=="yes")
{
if (MA.Available$WithinArrays)
{
Try(MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
if (WeightingType == "none")
Try (MA <- normalizeWithinArrays(RG,maLayout,method=WithinArrayNormalizationMethod))
else
Try(MA <- normalizeWithinArrays(RG,weights=RG$weights,maLayout,method=WithinArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAwithinArrays",MA,limmaGUIenvironment))
Try(MA.Available$WithinArrays <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinOnly","WithinOnly.Status" ,text=paste("Available (using ",WithinArrayNormalizationMethod,")",sep=""),font=.limmaGUIglobals$limmaGUIfontTree))
}
}
else
{
if (MA.Available$Raw)
{
Try(MA <- get("MAraw",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- MA.RG(RG))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAraw",MA,limmaGUIenvironment))
Try(MA.Available$Raw <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"Raw.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","Raw","Raw.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
Try(MA <- get("MA",envir=limmaGUIenvironment))
if (WhetherToNormalizeBetweenArrays=="yes")
{
if (WhetherToNormalizeWithinArrays=="yes")
{
if (MA.Available$Both)
{
Try(MA <- get("MAboth",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- normalizeBetweenArrays(MA,method=BetweenArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAboth",MA,limmaGUIenvironment))
Try(MA.Available$Both <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
else
{
if (MA.Available$BetweenArrays)
{
Try(MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- normalizeBetweenArrays(MA,method=BetweenArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAbetweenArrays",MA,limmaGUIenvironment))
Try(MA.Available$BetweenArrays <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
}
Try(tkconfigure(.limmaGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
AboutNormalization <- function()
{
Try(winTitle<-"About Normalization")
Try(message<-paste("Almost all cDNA data should be normalized within arrays.\n",
"The default method of print-tip-group loess should be suitable for most data.\n",
"If there is a significant difference in scale between the arrays (as seen by an M Box Plot by slide),\n",
"then the data should be normalized between arrays as well.\n\n",
"Use the M Box Plots to see the effects of the normalization.\n\n",
"The M Box Plot and the Color-Coded M A Plot both use the same normalization methods (from the\n",
"limma package) which are used in the linear model. Here, you have to normalize within all arrays\n",
"at once (which can be slow the first time), but the results will be recorded in the left status\n",
"window, and as long as you don't change the within-array normalization method, your data will not\n",
"need to be normalized again. If you ask for a plot or a linear model requiring normalized M and A\n",
"values, it should be much quicker the second time.\n",sep=""))
Try(ttAboutNormalization <- tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttAboutNormalization,winTitle))
Try(tkwm.deiconify(ttAboutNormalization))
Try(tkgrab.set(ttAboutNormalization))
Try(scr <- tkscrollbar(ttAboutNormalization, repeatinterval=5,
command=function(...)tkyview(txt,...)))
Try(txt <- tktext(ttAboutNormalization,bg="white",yscrollcommand=function(...)tkset(scr,...)))
Try(tkgrid(txt,scr))
Try(tkgrid.configure(scr,sticky="ns"))
Try(tkgrid.configure(txt,sticky="nsew"))
Try(tkinsert(txt,"end",message))
Try(tkconfigure(txt, state="disabled"))
Try(tkfocus(txt))
Try(onOK <- function() {Try(tkgrab.release(ttAboutNormalization));tkdestroy(ttAboutNormalization)})
Try(OK.but <- tkbutton(ttAboutNormalization,text=" Close ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(ttAboutNormalization,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid(tklabel(ttAboutNormalization,text=" ")))
Try(tkfocus(OK.but))
Try(tkwait.window(ttAboutNormalization))
}
ExportMvalues <- function()
{
Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(gal <- get("gal",envir=limmaGUIenvironment))
Try(if (NormalizedMADataWasImported==FALSE)
{
Try(Which <- WithinBetweenOrBoth("M"))
Try(if (Which=="") return())
Try(if (MA.Available[[Which]]==FALSE)
{
tkmessageBox(title="MA Object Unavailable",message="The MA object you requested is unavailable. Click on \"Normalize / Update M and A\" from the \"Normalization\" menu.")
return()
})
Try(if (Which=="Raw") MA <- get("MAraw",envir=limmaGUIenvironment))
Try(if (Which=="WithinArrays") MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(if (Which=="BetweenArrays") MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(if (Which=="Both") MA <- get("MAboth",envir=limmaGUIenvironment))
}
else
Try(MA <- get("MAimported",envir=limmaGUIenvironment)))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=paste(limmaDataSetNameText,"_M.xls",sep=""),filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if (!nchar(FileName)) return())
Try(len <- nchar(FileName))
if (len<=4)
Try(FileName <- paste(FileName,".xls",sep=""))
else if ((substring(FileName,len-3,len)!=".xls") && (substring(FileName,len-3,len)!=".txt"))
Try(FileName <- paste(FileName,".xls",sep=""))
Try(write.table(data.frame(gal,MA$M),file=FileName,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE))
}
ExportAvalues <- function()
{
Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(gal <- get("gal",envir=limmaGUIenvironment))
Try(if (NormalizedMADataWasImported==FALSE)
{
Try(Which <- WithinBetweenOrBoth("A"))
Try(if (Which=="") return())
Try(if (MA.Available[[Which]]==FALSE)
{
tkmessageBox(title="MA Object Unavailable",message="The MA object you requested is unavailable. Click on \"Normalize / Update M and A\" from the \"Normalization\" menu.")
return()
})
Try(if (Which=="Raw") MA <- get("MAraw",envir=limmaGUIenvironment))
Try(if (Which=="WithinArrays") MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(if (Which=="BetweenArrays") MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(if (Which=="Both") MA <- get("MAboth",envir=limmaGUIenvironment))
}
else
Try(MA <- get("MAimported",envir=limmaGUIenvironment)))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=paste(limmaDataSetNameText,"_A.xls"),filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if (!nchar(FileName)) return())
Try(len <- nchar(FileName))
if (len<=4)
Try(FileName <- paste(FileName,".xls",sep=""))
else if ((substring(FileName,len-3,len)!=".xls") && (substring(FileName,len-3,len)!=".txt"))
Try(FileName <- paste(FileName,".xls",sep=""))
Try(write.table(data.frame(gal,MA$A),file=FileName,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE))
}
WithinBetweenOrBoth <- function(MorA="M")
{
Try(ttWithinBetweenOrBoth <- tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttWithinBetweenOrBoth,paste("Export",MorA,"values.")))
Try(tkwm.deiconify(ttWithinBetweenOrBoth))
Try(tkgrab.set(ttWithinBetweenOrBoth))
Try(tkfocus(ttWithinBetweenOrBoth))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tklabel(ttWithinBetweenOrBoth,text=paste("Which",MorA,"values should be exported"),font=.limmaGUIglobals$limmaGUIfont2),tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tklabel(ttWithinBetweenOrBoth,text="as tab-delimited text?",font=.limmaGUIglobals$limmaGUIfont2),tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(WithinBetweenOrBothTcl <- tclVar("WithinArrays"))
Try(frame1 <- tkframe(ttWithinBetweenOrBoth,relief="groove",borderwidth="2"))
Try(tkgrid(tkradiobutton(frame1,text="Raw (Unnormalized)",variable=WithinBetweenOrBothTcl,value="Raw",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Within-Array Normalized",variable=WithinBetweenOrBothTcl,value="WithinArrays",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Between-Array Normalized",variable=WithinBetweenOrBothTcl,value="BetweenArrays",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Within-Array and Between-Array Normalized",variable=WithinBetweenOrBothTcl,value="Both",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),frame1))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkframeOKCancel <- tkframe(ttWithinBetweenOrBoth))
Try(ReturnVal <- "")
Try(onOK <- function() { Try(ReturnVal <<- tclvalue(WithinBetweenOrBothTcl)); Try(tkdestroy(ttWithinBetweenOrBoth));Try(tkfocus(.limmaGUIglobals$ttMain))})
Try(onCancel <- function() { Try(tkdestroy(ttWithinBetweenOrBoth));Try(ReturnVal <- "")})
Try(OK.but <- tkbutton(tkframeOKCancel,text=" OK ",command=onOK, font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <- tkbutton(tkframeOKCancel,text=" Cancel ",command=onCancel,font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframeOKCancel,text=" "),columnspan=2))
Try(tkgrid(OK.but,Cancel.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(tkframeOKCancel,text=" "),columnspan=2))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tkframeOKCancel))
Try(tkbind(ttWithinBetweenOrBoth, "<Destroy>", function() {Try(tkgrab.release(ttWithinBetweenOrBoth));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttWithinBetweenOrBoth))
return (ReturnVal)
}
GetBetweenArrayNormalizationMethod <- function()
{
Try(ttGetBetweenArrayNormalizationMethod<-tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttGetBetweenArrayNormalizationMethod,"Between-Array Normalization Method"))
Try(tkwm.deiconify(ttGetBetweenArrayNormalizationMethod))
Try(tkgrab.set(ttGetBetweenArrayNormalizationMethod))
Try(tkframe1 <- tkframe(ttGetBetweenArrayNormalizationMethod,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a method for between-array normalization.",font=.limmaGUIglobals$limmaGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(if (!exists("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(BetweenArrayNormalizationMethod <- "scale")
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
})
Try(BetweenArrayNormalizationMethod <- get("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(methnorm <- tclVar(BetweenArrayNormalizationMethod))
# Try(none.but <- tkradiobutton(tkframe2,text="None",variable=methnorm,value="none",font=.limmaGUIglobals$limmaGUIfont2))
Try(scale.but <- tkradiobutton(tkframe2,text="Scale",variable=methnorm,value="scale",font=.limmaGUIglobals$limmaGUIfont2))
Try(quantile.but <- tkradiobutton(tkframe2,text="Quantile",variable=methnorm,value="quantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Aquantile.but <- tkradiobutton(tkframe2,text="Aquantile",variable=methnorm,value="Aquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Gquantile.but <- tkradiobutton(tkframe2,text="Gquantile",variable=methnorm,value="Gquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Rquantile.but <- tkradiobutton(tkframe2,text="Rquantile",variable=methnorm,value="Rquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Tquantile.but <- tkradiobutton(tkframe2,text="Tquantile",variable=methnorm,value="Tquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(vsn.but <- tkradiobutton(tkframe2,text="VSN",variable=methnorm,value="vsn",font=.limmaGUIglobals$limmaGUIfont2))
# Try(tkgrid(none.but,column=2))
Try(tkgrid(scale.but,column=2))
Try(tkgrid(quantile.but,column=2))
Try(tkgrid(Aquantile.but,column=2))
Try(tkgrid(Gquantile.but,column=2))
Try(tkgrid(Rquantile.but,column=2))
Try(tkgrid(Tquantile.but,column=2))
Try(tkgrid(vsn.but,column=2))
# Try(tkgrid.configure(none.but,scale.but,quantile.but,Aquantile.but,Gquantile.but,Rquantile.but,Tquantile.but,vsn.but,sticky="w"))
Try(tkgrid.configure(scale.but,quantile.but,Aquantile.but,Gquantile.but,Rquantile.but,Tquantile.but,vsn.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(NewBetweenArrayNormalizationMethod <- "")
onOK <- function()
{
Try(NewBetweenArrayNormalizationMethod<<-tclvalue(methnorm));
Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));
Try(tkdestroy(ttGetBetweenArrayNormalizationMethod))
Try(if (NewBetweenArrayNormalizationMethod==BetweenArrayNormalizationMethod)
return())
Try(BetweenArrayNormalizationMethod <- NewBetweenArrayNormalizationMethod)
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(MA.Available$Both <- FALSE)
Try(MA.Available$BetweenArrayNormalizationMethods <- FALSE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));Try(tkdestroy(ttGetBetweenArrayNormalizationMethod));NewBetweenArrayNormalizationMethod<-"";Try(tkfocus(.limmaGUIglobals$ttMain))},font=.limmaGUIglobals$limmaGUIfont2))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(help("normalizeBetweenArrays",help_type="html")),font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetBetweenArrayNormalizationMethod, "<Return>",onOK))
Try(tkbind(ttGetBetweenArrayNormalizationMethod, "<Destroy>", function() {Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttGetBetweenArrayNormalizationMethod))
Try(tkdestroy(ttGetBetweenArrayNormalizationMethod))
# This return value below is not used. The function above is used for its effect
# on BetweenArrayNormalizationMethod in limmaGUIenvironment
return(NewBetweenArrayNormalizationMethod)
}
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Defines functions GetBetweenArrayNormalizationMethod WithinBetweenOrBoth ExportAvalues ExportMvalues AboutNormalization NormalizeNow GetWithinArrayNormalizationMethod
Documented in AboutNormalization ExportAvalues ExportMvalues GetBetweenArrayNormalizationMethod GetWithinArrayNormalizationMethod NormalizeNow WithinBetweenOrBoth
GetWithinArrayNormalizationMethod <- function()
{
Try(ttGetWithinArrayNormalizationMethod<-tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttGetWithinArrayNormalizationMethod,"Within-Array Normalization Method"))
Try(tkwm.deiconify(ttGetWithinArrayNormalizationMethod))
Try(tkgrab.set(ttGetWithinArrayNormalizationMethod))
Try(tkframe1 <- tkframe(ttGetWithinArrayNormalizationMethod,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a method for within-array normalization.",font=.limmaGUIglobals$limmaGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(methnorm <- tclVar(WithinArrayNormalizationMethod))
# Try(none.but <- tkradiobutton(tkframe2,text="None",variable=methnorm,value="none",font=.limmaGUIglobals$limmaGUIfont2))
Try(median.but <- tkradiobutton(tkframe2,text="Median",variable=methnorm,value="median",font=.limmaGUIglobals$limmaGUIfont2))
Try(global.but <- tkradiobutton(tkframe2,text="Global loess",variable=methnorm,value="loess",font=.limmaGUIglobals$limmaGUIfont2))
Try(printtip.but <- tkradiobutton(tkframe2,text="Print-tip group loess",variable=methnorm,value="printtiploess",font=.limmaGUIglobals$limmaGUIfont2))
Try(composite.but <- tkradiobutton(tkframe2,text="Composite",variable=methnorm,value="composite",font=.limmaGUIglobals$limmaGUIfont2))
Try(robustspline.but <- tkradiobutton(tkframe2,text="Robust Spline",variable=methnorm,value="robustspline",font=.limmaGUIglobals$limmaGUIfont2))
# Try(tkgrid(none.but,column=2))
Try(tkgrid(median.but,column=2))
Try(tkgrid(global.but,column=2))
Try(tkgrid(printtip.but,column=2))
Try(tkgrid(composite.but,column=2))
Try(tkgrid(robustspline.but,column=2))
# Try(tkgrid.configure(none.but,median.but,global.but,printtip.but,composite.but,robustspline.but,sticky="w"))
Try(tkgrid.configure(median.but,global.but,printtip.but,composite.but,robustspline.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(NewNormalizationMethod <- "")
onOK <- function()
{
Try(NewNormalizationMethod<<-tclvalue(methnorm));
Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));
Try(tkdestroy(ttGetWithinArrayNormalizationMethod))
Try(if (NewNormalizationMethod==WithinArrayNormalizationMethod)
return())
Try(WithinArrayNormalizationMethod <- NewNormalizationMethod)
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(MA.Available$WithinArrays <- FALSE)
Try(MA.Available$Both <- FALSE)
Try(MA.Available$BetweenArrays <- FALSE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinOnly","WithinOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));Try(tkdestroy(ttGetWithinArrayNormalizationMethod));NewNormalizationMethod<-"";Try(tkfocus(.limmaGUIglobals$ttMain))},font=.limmaGUIglobals$limmaGUIfont2))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(help("normalizeWithinArrays",help_type="html")),font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetWithinArrayNormalizationMethod, "<Return>",onOK))
Try(tkbind(ttGetWithinArrayNormalizationMethod, "<Destroy>", function() {Try(tkgrab.release(ttGetWithinArrayNormalizationMethod));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttGetWithinArrayNormalizationMethod))
Try(tkdestroy(ttGetWithinArrayNormalizationMethod))
# This return value below is not used. The function above is used for its effect
# on WithinArrayNormalizationMethod in limmaGUIenvironment
return(NewNormalizationMethod)
}
NormalizeNow <- function()
{
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(ArraysLoaded <- get("ArraysLoaded", envir=limmaGUIenvironment))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
if (ArraysLoaded==FALSE)
{
Try(tkmessageBox(title="Normalization",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.limmaGUIglobals$ttMain))
return()
}
if (NormalizedMADataWasImported==TRUE)
{
Try(tkmessageBox(title="Normalization",message="Normalized data was imported. Impossible to recover raw data to renormalize.",type="ok",icon="error"))
Try(tkfocus(.limmaGUIglobals$ttMain))
return()
}
Try(RG <- get("RG",envir=limmaGUIenvironment))
Try(SetLayoutParamReturnVal <- 1)
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(if (length(maLayout)==0) SetLayoutParamReturnVal <-Try(SetLayoutParameters()))
Try(if (SetLayoutParamReturnVal==0) return())
Try(maLayout <- get("maLayout",envir=limmaGUIenvironment))
Try(NormalizeWithinArraysMB <-tkmessageBox(title="Normalization Within Arrays",message="Normalize Within Arrays?",type="yesnocancel",icon="question",default="yes"))
Try(WhetherToNormalizeWithinArrays <- tclvalue(NormalizeWithinArraysMB))
if (WhetherToNormalizeWithinArrays=="cancel")
return()
Try(if (WhetherToNormalizeWithinArrays=="yes")
{
Try(GetWithinArrayNormMethodVal<- GetWithinArrayNormalizationMethod())
Try(if (GetWithinArrayNormMethodVal=="") return())
})
Try(NormalizeBetweenArraysMB <-tkmessageBox(title="Normalization Between Arrays",message="Normalize Between Arrays?",type="yesnocancel",icon="question",default="no"))
Try(WhetherToNormalizeBetweenArrays <- tclvalue(NormalizeBetweenArraysMB))
if (WhetherToNormalizeBetweenArrays=="cancel")
return()
Try(if (WhetherToNormalizeBetweenArrays=="yes")
{
Try(GetBetweenArrayNormMethodVal<- GetBetweenArrayNormalizationMethod())
Try(if (GetBetweenArrayNormMethodVal=="") return())
})
Try(tkconfigure(.limmaGUIglobals$ttMain,cursor="watch"))
Try(tkfocus(.limmaGUIglobals$ttMain))
Try(WeightingType <- get("WeightingType",envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(if (!exists("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(WithinArrayNormalizationMethod <- "printtiploess")
Try(assign("WithinArrayNormalizationMethod",WithinArrayNormalizationMethod,limmaGUIenvironment))
})
Try(WithinArrayNormalizationMethod <- get("WithinArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(if (!exists("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(BetweenArrayNormalizationMethod <- "scale")
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
})
Try(BetweenArrayNormalizationMethod <- get("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
if (WhetherToNormalizeWithinArrays=="yes")
{
if (MA.Available$WithinArrays)
{
Try(MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
if (WeightingType == "none")
Try (MA <- normalizeWithinArrays(RG,maLayout,method=WithinArrayNormalizationMethod))
else
Try(MA <- normalizeWithinArrays(RG,weights=RG$weights,maLayout,method=WithinArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAwithinArrays",MA,limmaGUIenvironment))
Try(MA.Available$WithinArrays <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinOnly","WithinOnly.Status" ,text=paste("Available (using ",WithinArrayNormalizationMethod,")",sep=""),font=.limmaGUIglobals$limmaGUIfontTree))
}
}
else
{
if (MA.Available$Raw)
{
Try(MA <- get("MAraw",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- MA.RG(RG))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAraw",MA,limmaGUIenvironment))
Try(MA.Available$Raw <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"Raw.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","Raw","Raw.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
Try(MA <- get("MA",envir=limmaGUIenvironment))
if (WhetherToNormalizeBetweenArrays=="yes")
{
if (WhetherToNormalizeWithinArrays=="yes")
{
if (MA.Available$Both)
{
Try(MA <- get("MAboth",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- normalizeBetweenArrays(MA,method=BetweenArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAboth",MA,limmaGUIenvironment))
Try(MA.Available$Both <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
else
{
if (MA.Available$BetweenArrays)
{
Try(MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(assign("MA",MA,limmaGUIenvironment))
}
else
{
Try (MA <- normalizeBetweenArrays(MA,method=BetweenArrayNormalizationMethod))
Try(assign("MA",MA,limmaGUIenvironment))
Try(assign("MAbetweenArrays",MA,limmaGUIenvironment))
Try(MA.Available$BetweenArrays <- TRUE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Available",font=.limmaGUIglobals$limmaGUIfontTree))
}
}
}
Try(tkconfigure(.limmaGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
AboutNormalization <- function()
{
Try(winTitle<-"About Normalization")
Try(message<-paste("Almost all cDNA data should be normalized within arrays.\n",
"The default method of print-tip-group loess should be suitable for most data.\n",
"If there is a significant difference in scale between the arrays (as seen by an M Box Plot by slide),\n",
"then the data should be normalized between arrays as well.\n\n",
"Use the M Box Plots to see the effects of the normalization.\n\n",
"The M Box Plot and the Color-Coded M A Plot both use the same normalization methods (from the\n",
"limma package) which are used in the linear model. Here, you have to normalize within all arrays\n",
"at once (which can be slow the first time), but the results will be recorded in the left status\n",
"window, and as long as you don't change the within-array normalization method, your data will not\n",
"need to be normalized again. If you ask for a plot or a linear model requiring normalized M and A\n",
"values, it should be much quicker the second time.\n",sep=""))
Try(ttAboutNormalization <- tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttAboutNormalization,winTitle))
Try(tkwm.deiconify(ttAboutNormalization))
Try(tkgrab.set(ttAboutNormalization))
Try(scr <- tkscrollbar(ttAboutNormalization, repeatinterval=5,
command=function(...)tkyview(txt,...)))
Try(txt <- tktext(ttAboutNormalization,bg="white",yscrollcommand=function(...)tkset(scr,...)))
Try(tkgrid(txt,scr))
Try(tkgrid.configure(scr,sticky="ns"))
Try(tkgrid.configure(txt,sticky="nsew"))
Try(tkinsert(txt,"end",message))
Try(tkconfigure(txt, state="disabled"))
Try(tkfocus(txt))
Try(onOK <- function() {Try(tkgrab.release(ttAboutNormalization));tkdestroy(ttAboutNormalization)})
Try(OK.but <- tkbutton(ttAboutNormalization,text=" Close ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(ttAboutNormalization,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid(tklabel(ttAboutNormalization,text=" ")))
Try(tkfocus(OK.but))
Try(tkwait.window(ttAboutNormalization))
}
ExportMvalues <- function()
{
Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(gal <- get("gal",envir=limmaGUIenvironment))
Try(if (NormalizedMADataWasImported==FALSE)
{
Try(Which <- WithinBetweenOrBoth("M"))
Try(if (Which=="") return())
Try(if (MA.Available[[Which]]==FALSE)
{
tkmessageBox(title="MA Object Unavailable",message="The MA object you requested is unavailable. Click on \"Normalize / Update M and A\" from the \"Normalization\" menu.")
return()
})
Try(if (Which=="Raw") MA <- get("MAraw",envir=limmaGUIenvironment))
Try(if (Which=="WithinArrays") MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(if (Which=="BetweenArrays") MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(if (Which=="Both") MA <- get("MAboth",envir=limmaGUIenvironment))
}
else
Try(MA <- get("MAimported",envir=limmaGUIenvironment)))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=paste(limmaDataSetNameText,"_M.xls",sep=""),filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if (!nchar(FileName)) return())
Try(len <- nchar(FileName))
if (len<=4)
Try(FileName <- paste(FileName,".xls",sep=""))
else if ((substring(FileName,len-3,len)!=".xls") && (substring(FileName,len-3,len)!=".txt"))
Try(FileName <- paste(FileName,".xls",sep=""))
Try(write.table(data.frame(gal,MA$M),file=FileName,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE))
}
ExportAvalues <- function()
{
Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=limmaGUIenvironment))
Try(NormalizedMADataWasImported<- get("NormalizedMADataWasImported", envir=limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(gal <- get("gal",envir=limmaGUIenvironment))
Try(if (NormalizedMADataWasImported==FALSE)
{
Try(Which <- WithinBetweenOrBoth("A"))
Try(if (Which=="") return())
Try(if (MA.Available[[Which]]==FALSE)
{
tkmessageBox(title="MA Object Unavailable",message="The MA object you requested is unavailable. Click on \"Normalize / Update M and A\" from the \"Normalization\" menu.")
return()
})
Try(if (Which=="Raw") MA <- get("MAraw",envir=limmaGUIenvironment))
Try(if (Which=="WithinArrays") MA <- get("MAwithinArrays",envir=limmaGUIenvironment))
Try(if (Which=="BetweenArrays") MA <- get("MAbetweenArrays",envir=limmaGUIenvironment))
Try(if (Which=="Both") MA <- get("MAboth",envir=limmaGUIenvironment))
}
else
Try(MA <- get("MAimported",envir=limmaGUIenvironment)))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=paste(limmaDataSetNameText,"_A.xls"),filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if (!nchar(FileName)) return())
Try(len <- nchar(FileName))
if (len<=4)
Try(FileName <- paste(FileName,".xls",sep=""))
else if ((substring(FileName,len-3,len)!=".xls") && (substring(FileName,len-3,len)!=".txt"))
Try(FileName <- paste(FileName,".xls",sep=""))
Try(write.table(data.frame(gal,MA$A),file=FileName,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE))
}
WithinBetweenOrBoth <- function(MorA="M")
{
Try(ttWithinBetweenOrBoth <- tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttWithinBetweenOrBoth,paste("Export",MorA,"values.")))
Try(tkwm.deiconify(ttWithinBetweenOrBoth))
Try(tkgrab.set(ttWithinBetweenOrBoth))
Try(tkfocus(ttWithinBetweenOrBoth))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tklabel(ttWithinBetweenOrBoth,text=paste("Which",MorA,"values should be exported"),font=.limmaGUIglobals$limmaGUIfont2),tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tklabel(ttWithinBetweenOrBoth,text="as tab-delimited text?",font=.limmaGUIglobals$limmaGUIfont2),tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(WithinBetweenOrBothTcl <- tclVar("WithinArrays"))
Try(frame1 <- tkframe(ttWithinBetweenOrBoth,relief="groove",borderwidth="2"))
Try(tkgrid(tkradiobutton(frame1,text="Raw (Unnormalized)",variable=WithinBetweenOrBothTcl,value="Raw",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Within-Array Normalized",variable=WithinBetweenOrBothTcl,value="WithinArrays",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Between-Array Normalized",variable=WithinBetweenOrBothTcl,value="BetweenArrays",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tkradiobutton(frame1,text="Within-Array and Between-Array Normalized",variable=WithinBetweenOrBothTcl,value="Both",font=.limmaGUIglobals$limmaGUIfont2),sticky="w"))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),frame1))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" ")))
Try(tkframeOKCancel <- tkframe(ttWithinBetweenOrBoth))
Try(ReturnVal <- "")
Try(onOK <- function() { Try(ReturnVal <<- tclvalue(WithinBetweenOrBothTcl)); Try(tkdestroy(ttWithinBetweenOrBoth));Try(tkfocus(.limmaGUIglobals$ttMain))})
Try(onCancel <- function() { Try(tkdestroy(ttWithinBetweenOrBoth));Try(ReturnVal <- "")})
Try(OK.but <- tkbutton(tkframeOKCancel,text=" OK ",command=onOK, font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <- tkbutton(tkframeOKCancel,text=" Cancel ",command=onCancel,font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframeOKCancel,text=" "),columnspan=2))
Try(tkgrid(OK.but,Cancel.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(tkframeOKCancel,text=" "),columnspan=2))
Try(tkgrid(tklabel(ttWithinBetweenOrBoth,text=" "),tkframeOKCancel))
Try(tkbind(ttWithinBetweenOrBoth, "<Destroy>", function() {Try(tkgrab.release(ttWithinBetweenOrBoth));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttWithinBetweenOrBoth))
return (ReturnVal)
}
GetBetweenArrayNormalizationMethod <- function()
{
Try(ttGetBetweenArrayNormalizationMethod<-tktoplevel(.limmaGUIglobals$ttMain))
Try(tkwm.title(ttGetBetweenArrayNormalizationMethod,"Between-Array Normalization Method"))
Try(tkwm.deiconify(ttGetBetweenArrayNormalizationMethod))
Try(tkgrab.set(ttGetBetweenArrayNormalizationMethod))
Try(tkframe1 <- tkframe(ttGetBetweenArrayNormalizationMethod,borderwidth=2))
Try(tkframe2 <- tkframe(tkframe1,relief="groove",borderwidth=2))
Try(tkframe4<-tkframe(tkframe1,borderwidth=2))
Try(tkgrid(tklabel(tkframe1,text=" ")))
Try(tkgrid(tklabel(tkframe2,text="Choose a method for between-array normalization.",font=.limmaGUIglobals$limmaGUIfont2),column=2,rowspan=1,columnspan=2,sticky="w"))
Try(if (!exists("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
{
Try(BetweenArrayNormalizationMethod <- "scale")
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
})
Try(BetweenArrayNormalizationMethod <- get("BetweenArrayNormalizationMethod",envir=limmaGUIenvironment))
Try(methnorm <- tclVar(BetweenArrayNormalizationMethod))
# Try(none.but <- tkradiobutton(tkframe2,text="None",variable=methnorm,value="none",font=.limmaGUIglobals$limmaGUIfont2))
Try(scale.but <- tkradiobutton(tkframe2,text="Scale",variable=methnorm,value="scale",font=.limmaGUIglobals$limmaGUIfont2))
Try(quantile.but <- tkradiobutton(tkframe2,text="Quantile",variable=methnorm,value="quantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Aquantile.but <- tkradiobutton(tkframe2,text="Aquantile",variable=methnorm,value="Aquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Gquantile.but <- tkradiobutton(tkframe2,text="Gquantile",variable=methnorm,value="Gquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Rquantile.but <- tkradiobutton(tkframe2,text="Rquantile",variable=methnorm,value="Rquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(Tquantile.but <- tkradiobutton(tkframe2,text="Tquantile",variable=methnorm,value="Tquantile",font=.limmaGUIglobals$limmaGUIfont2))
Try(vsn.but <- tkradiobutton(tkframe2,text="VSN",variable=methnorm,value="vsn",font=.limmaGUIglobals$limmaGUIfont2))
# Try(tkgrid(none.but,column=2))
Try(tkgrid(scale.but,column=2))
Try(tkgrid(quantile.but,column=2))
Try(tkgrid(Aquantile.but,column=2))
Try(tkgrid(Gquantile.but,column=2))
Try(tkgrid(Rquantile.but,column=2))
Try(tkgrid(Tquantile.but,column=2))
Try(tkgrid(vsn.but,column=2))
# Try(tkgrid.configure(none.but,scale.but,quantile.but,Aquantile.but,Gquantile.but,Rquantile.but,Tquantile.but,vsn.but,sticky="w"))
Try(tkgrid.configure(scale.but,quantile.but,Aquantile.but,Gquantile.but,Rquantile.but,Tquantile.but,vsn.but,sticky="w"))
Try(tkgrid(tkframe2))
Try(NewBetweenArrayNormalizationMethod <- "")
onOK <- function()
{
Try(NewBetweenArrayNormalizationMethod<<-tclvalue(methnorm));
Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));
Try(tkdestroy(ttGetBetweenArrayNormalizationMethod))
Try(if (NewBetweenArrayNormalizationMethod==BetweenArrayNormalizationMethod)
return())
Try(BetweenArrayNormalizationMethod <- NewBetweenArrayNormalizationMethod)
Try(assign("BetweenArrayNormalizationMethod",BetweenArrayNormalizationMethod,limmaGUIenvironment))
Try(MA.Available <- get("MA.Available",envir=limmaGUIenvironment))
Try(MA.Available$Both <- FALSE)
Try(MA.Available$BetweenArrayNormalizationMethods <- FALSE)
Try(assign("MA.Available",MA.Available,limmaGUIenvironment))
Try(tkdelete(.limmaGUIglobals$mainTree,"WithinAndBetween.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","WithinAndBetween","WithinAndBetween.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkdelete(.limmaGUIglobals$mainTree,"BetweenOnly.Status"))
Try(tkinsert(.limmaGUIglobals$mainTree,"end","BetweenOnly","BetweenOnly.Status" ,text="Not Available",font=.limmaGUIglobals$limmaGUIfontTree))
Try(tkfocus(.limmaGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(tkframe4,text=" OK ",command=onOK,font=.limmaGUIglobals$limmaGUIfont2))
Try(Cancel.but <-tkbutton(tkframe4,text=" Cancel ",command=function(){Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));Try(tkdestroy(ttGetBetweenArrayNormalizationMethod));NewBetweenArrayNormalizationMethod<-"";Try(tkfocus(.limmaGUIglobals$ttMain))},font=.limmaGUIglobals$limmaGUIfont2))
Try(Help.but <- tkbutton(tkframe4,text=" Help ",command=function()Try(help("normalizeBetweenArrays",help_type="html")),font=.limmaGUIglobals$limmaGUIfont2))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(OK.but,Cancel.but,Help.but))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="e"))
Try(tkgrid.configure(Help.but,sticky="e"))
Try(tkgrid(tklabel(tkframe4,text=" ")))
Try(tkgrid(tkframe4))
Try(tkgrid(tkframe1))
Try(tkfocus(OK.but))
Try(tkbind(ttGetBetweenArrayNormalizationMethod, "<Return>",onOK))
Try(tkbind(ttGetBetweenArrayNormalizationMethod, "<Destroy>", function() {Try(tkgrab.release(ttGetBetweenArrayNormalizationMethod));Try(tkfocus(.limmaGUIglobals$ttMain))}))
Try(tkwait.window(ttGetBetweenArrayNormalizationMethod))
Try(tkdestroy(ttGetBetweenArrayNormalizationMethod))
# This return value below is not used. The function above is used for its effect
# on BetweenArrayNormalizationMethod in limmaGUIenvironment
return(NewBetweenArrayNormalizationMethod)
}
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