Nothing
`plotQC` <-
function(x,file="target_vs_blank.pdf",arrays2rm=c("protein")){
x <- remove.arrays(x,param="target",arrays2rm=arrays2rm)
#inc.run <- levels(as.factor(x[[3]]["incubation_run",]))
inc.run <- unique(x[[3]]["incubation_run",])
ctrl.lines <- which ( x[[4]][,"sample_type"]=="control")
controls <- unique(x[[4]][ctrl.lines,"sample"])
pdf(file=file)
for (j in seq(along=inc.run)){
## define columns of a single incubation run
run.cols <- which((x[[3]]["incubation_run",])==inc.run[j])
## select data of a single incubation run
temp.dat <- x[[1]][,run.cols]
temp.arrays <- x[[3]] [,run.cols]
blk.col <- grep("lank$",temp.arrays["target",])
for (i in 1:ncol(temp.dat)){
#ctrl.lines <- which ( x[[4]][,"sample_type"]=="control")
temp.dat <- x[[1]][ctrl.lines,run.cols]
temp.anno <- x[[4]][ctrl.lines,]
par(lwd=2)
plot(x=NULL,y=NULL
, main=c(paste("target: ",temp.arrays["target",i]," Ab: ",temp.arrays["AB_ID",i])
,paste("incubation run: ",inc.run[j]))
,xlab="concentration",ylab="signal intensity [a.u.]"
,ylim=c(0,max(c(temp.dat[,i],temp.dat[,blk.col])))
,xlim=c(0,max(x[[4]][ctrl.lines,"concentration"])))
for (k in seq(along=controls)){
ctrl.lines.ii <- which( temp.anno[,"sample"]==controls[k])
points(x=temp.anno[ctrl.lines.ii,"concentration"],y=temp.dat[ctrl.lines.ii,i]
,pch=k+1,col=k+1)
}
points ( x[[4]][ctrl.lines,"concentration"],temp.dat[,blk.col],
col=1,pch=1)
legend("topleft",col=c(1,(seq(along=controls)+1)),pch=c(1,(seq(along=controls)+1))
,legend=c("blank",as.character(controls)))
}
}
dev.off()
}
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