inst/extdata/filter_unsp2.R

In maGUI: A Graphical User Interface for Microarray Data Analysis and Annotation

filter_unsp<-function(h,...){
	stdev_filt<-function(h,h2,h3,h4,h5,...){
		ts_name=h;ts_val=h2;children<-h3;r_choice=h4;std<-as.numeric(h5);
		if(ts_name=="Affymetrix"){
			dat2Affy.m<-dat2Affy.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(dat2Affy.m)
			i<-rsd>=std
			dat.f<-dat2Affy.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Affy[[ts_val]]<<-fit2
			dat2Affy.f<-fit2
			ps1<-as.data.frame(dat2Affy.f)	
			rownames(ps1)<-rownames(fit2)
			dat2Affy.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_affy_filt<-tclArray()
			for(i in 0:dim(dat2Affy.f2)[1]){ for(j in 0:dim(dat2Affy.f2)[2]){ 
				if(i==0){ ta_affy_filt[[i,j]]<-colnames(dat2Affy.f2)[j] } else { 
				if(j==0){ ta_affy_filt[[i,j]]<-rownames(dat2Affy.f2)[i] } else {
				tem<-dat2Affy.f2[i,j]
				ta_affy_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			dat2Affy.f3[[ts_val]]<<-dat2Affy.f2
			ta_affy_filt2[[ts_val]]<<-ta_affy_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(dat2Affy.f)!=0){
				err<-try({
					ttx<-topTable(dat2Affy.f,number=nrow(dat2Affy.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(dat2Affy.m)==TRUE)]
					dat2Affy.s<-dat2Affy.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(dat2Affy.f,number=nrow(dat2Affy.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(dat2Affy.m)==TRUE)])
					dat2Affy.s<-dat2Affy.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			dat2Affy.s2<-dat2Affy.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_affy_stat<-tclArray()
			for(i in 0:dim(dat2Affy.s2)[1]){ for(j in 0:dim(dat2Affy.s2)[2]){ 
				if(i==0){ ta_affy_stat[[i,j]]<-colnames(dat2Affy.s2)[j] } else { 
				if(j==0){ ta_affy_stat[[i,j]]<-rownames(dat2Affy.s2)[i] } else {
				tem<-dat2Affy.s2[i,j]
				ta_affy_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			dat2Affy.s3[[ts_val]]<<-dat2Affy.s2			
			ta_affy_stat2[[ts_val]]<<-ta_affy_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Agilent-OneColor"){
			datAgOne2.m<-datAgOne2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(datAgOne2.m)
			i<-rsd>=std
			dat.f<-datAgOne2.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Ag1[[ts_val]]<<-fit2
			datAgOne2.f<-fit2
			ps1<-as.data.frame(datAgOne2.f)	
			rownames(ps1)<-rownames(fit2)
			datAgOne2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ag1_filt<-tclArray()
			for(i in 0:dim(datAgOne2.f2)[1]){ for(j in 0:dim(datAgOne2.f2)[2]){ 
				if(i==0){ ta_ag1_filt[[i,j]]<-colnames(datAgOne2.f2)[j] } else { 
				if(j==0){ ta_ag1_filt[[i,j]]<-rownames(datAgOne2.f2)[i] } else {
				tem<-datAgOne2.f2[i,j]
				ta_ag1_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datAgOne2.f3[[ts_val]]<<-datAgOne2.f2
			ta_ag1_filt2[[ts_val]]<<-ta_ag1_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datAgOne2.f)!=0){
				err<-try({
					ttx<-topTable(datAgOne2.f,number=nrow(datAgOne2.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgOne2.m)==TRUE)]
					datAgOne2.s<-datAgOne2.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datAgOne2.f,number=nrow(datAgOne2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgOne2.m)==TRUE)])
					datAgOne2.s<-datAgOne2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datAgOne2.s2<-datAgOne2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ag1_stat<-tclArray()
			for(i in 0:dim(datAgOne2.s2)[1]){ for(j in 0:dim(datAgOne2.s2)[2]){ 
				if(i==0){ ta_ag1_stat[[i,j]]<-colnames(datAgOne2.s2)[j] } else { 
				if(j==0){ ta_ag1_stat[[i,j]]<-rownames(datAgOne2.s2)[i] } else {
				tem<-datAgOne2.s2[i,j]
				ta_ag1_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datAgOne2.s3[[ts_val]]<<-datAgOne2.s2			
			ta_ag1_stat2[[ts_val]]<<-ta_ag1_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Agilent-TwoColor"){
			datAgTwo2.m<-datAgTwo2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(datAgTwo2.m)
			i<-rsd>=std
			dat.f<-datAgTwo2.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Ag2[[ts_val]]<<-fit2
			datAgTwo2.f<-fit2
			ps1<-as.data.frame(datAgTwo2.f)	
			rownames(ps1)<-rownames(fit2)
			datAgTwo2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ag2_filt<-tclArray()
			for(i in 0:dim(datAgTwo2.f2)[1]){ for(j in 0:dim(datAgTwo2.f2)[2]){ 
				if(i==0){ ta_ag2_filt[[i,j]]<-colnames(datAgTwo2.f2)[j] } else { 
				if(j==0){ ta_ag2_filt[[i,j]]<-rownames(datAgTwo2.f2)[i] } else {
				tem<-datAgTwo2.f2[i,j]
				ta_ag2_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datAgTwo2.f3[[ts_val]]<<-datAgTwo2.f2
			ta_ag2_filt2[[ts_val]]<<-ta_ag2_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datAgTwo2.f)!=0){
				err<-try({
						ttx<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)]
						datAgTwo2.s<-datAgTwo2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)])
					datAgTwo2.s<-datAgTwo2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datAgTwo2.s2<-datAgTwo2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ag2_stat<-tclArray()
			for(i in 0:dim(datAgTwo2.s2)[1]){ for(j in 0:dim(datAgTwo2.s2)[2]){ 
				if(i==0){ ta_ag2_stat[[i,j]]<-colnames(datAgTwo2.s2)[j] } else { 
				if(j==0){ ta_ag2_stat[[i,j]]<-rownames(datAgTwo2.s2)[i] } else {
				tem<-datAgTwo2.s2[i,j]
				ta_ag2_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datAgTwo2.s3[[ts_val]]<<-datAgTwo2.s2			
			ta_ag2_stat2[[ts_val]]<<-ta_ag2_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Illumina-Beadarray"){
			datIllBA2.m<-datIllBA2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(datIllBA2.m)
			i<-rsd>=std
			dat.f<-datIllBA2.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Il_B[[ts_val]]<<-fit2
			datIllBA2.f<-fit2
			ps1<-as.data.frame(datIllBA2.f)	
			rownames(ps1)<-rownames(fit2)
			datIllBA2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ilb_filt<-tclArray()
			for(i in 0:dim(datIllBA2.f2)[1]){ for(j in 0:dim(datIllBA2.f2)[2]){ 
				if(i==0){ ta_ilb_filt[[i,j]]<-colnames(datIllBA2.f2)[j] } else { 
				if(j==0){ ta_ilb_filt[[i,j]]<-rownames(datIllBA2.f2)[i] } else {
				tem<-datIllBA2.f2[i,j]
				ta_ilb_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datIllBA2.f3[[ts_val]]<<-datIllBA2.f2
			ta_ilb_filt2[[ts_val]]<<-ta_ilb_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datIllBA2.f)!=0){
				err<-try({
						ttx<-topTable(datIllBA2.f,number=nrow(datIllBA2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datIllBA2.m1)==TRUE)]
						datIllBA2.s<-datIllBA2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datIllBA2.f,number=nrow(datIllBA2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datIllBA2.m1)==TRUE)])
					datIllBA2.s<-datIllBA2.m1[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datIllBA2.s2<-datIllBA2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ilb_stat<-tclArray()
			for(i in 0:dim(datIllBA2.s2)[1]){ for(j in 0:dim(datIllBA2.s2)[2]){ 
				if(i==0){ ta_ilb_stat[[i,j]]<-colnames(datIllBA2.s2)[j] } else { 
				if(j==0){ ta_ilb_stat[[i,j]]<-rownames(datIllBA2.s2)[i] } else {
				tem<-datIllBA2.s2[i,j]
				ta_ilb_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datIllBA2.s3[[ts_val]]<<-datIllBA2.s2			
			ta_ilb_stat2[[ts_val]]<<-ta_ilb_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Illumina-Lumi"){
			lumi_NQ.m<-lumi_NQ.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(lumi_NQ.m)
			i<-rsd>=std
			dat.f<-lumi_NQ.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Il_L[[ts_val]]<<-fit2
			lumi_NQ.f<-fit2
			ps1<-as.data.frame(lumi_NQ.f)	
			rownames(ps1)<-rownames(fit2)
			lumi_NQ.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ill_filt<-tclArray()
			for(i in 0:dim(lumi_NQ.f2)[1]){ for(j in 0:dim(lumi_NQ.f2)[2]){ 
				if(i==0){ ta_ill_filt[[i,j]]<-colnames(lumi_NQ.f2)[j] } else { 
				if(j==0){ ta_ill_filt[[i,j]]<-rownames(lumi_NQ.f2)[i] } else {
				tem<-lumi_NQ.f2[i,j]
				ta_ill_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			lumi_NQ.f3[[ts_val]]<<-lumi_NQ.f2
			ta_ill_filt2[[ts_val]]<<-ta_ill_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(lumi_NQ.f)!=0){
				err<-try({
						ttx<-topTable(lumi_NQ.f,number=nrow(lumi_NQ.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(lumi_NQ.m)==TRUE)]
						lumi_NQ.s<-lumi_NQ.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(lumi_NQ.f,number=nrow(lumi_NQ.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(lumi_NQ.m)==TRUE)])
					lumi_NQ.s<-lumi_NQ.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			lumi_NQ.s2<-lumi_NQ.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ill_stat<-tclArray()
			for(i in 0:dim(lumi_NQ.s2)[1]){ for(j in 0:dim(lumi_NQ.s2)[2]){ 
				if(i==0){ ta_ill_stat[[i,j]]<-colnames(lumi_NQ.s2)[j] } else { 
				if(j==0){ ta_ill_stat[[i,j]]<-rownames(lumi_NQ.s2)[i] } else {
				tem<-lumi_NQ.s2[i,j]
				ta_ill_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			lumi_NQ.s3[[ts_val]]<<-lumi_NQ.s2			
			ta_ill_stat2[[ts_val]]<<-ta_ill_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Nimblegen"){
			data.matrix_Nimblegen2.m<-data.matrix_Nimblegen2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			rsd<-rowSds(data.matrix_Nimblegen2.m)
			i<-rsd>=std
			dat.f<-data.matrix_Nimblegen2.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_N[[ts_val]]<<-fit2
			data.matrix_Nimblegen2.f<-fit2
			ps1<-as.data.frame(data.matrix_Nimblegen2.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrix_Nimblegen2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_nbl_filt<-tclArray()
			for(i in 0:dim(data.matrix_Nimblegen2.f2)[1]){ for(j in 0:dim(data.matrix_Nimblegen2.f2)[2]){ 
				if(i==0){ ta_nbl_filt[[i,j]]<-colnames(data.matrix_Nimblegen2.f2)[j] } else { 
				if(j==0){ ta_nbl_filt[[i,j]]<-rownames(data.matrix_Nimblegen2.f2)[i] } else {
				tem<-data.matrix_Nimblegen2.f2[i,j]
				ta_nbl_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrix_Nimblegen2.f3[[ts_val]]<<-data.matrix_Nimblegen2.f2
			ta_nbl_filt2[[ts_val]]<<-ta_nbl_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrix_Nimblegen2.f)!=0){
				err<-try({
						ttx<-topTable(data.matrix_Nimblegen2.f,number=nrow(data.matrix_Nimblegen2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_Nimblegen2.m)==TRUE)]
						data.matrix_Nimblegen2.s<-data.matrix_Nimblegen2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrix_Nimblegen2.f,number=nrow(data.matrix_Nimblegen2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_Nimblegen2.m)==TRUE)])
					data.matrix_Nimblegen2.s<-data.matrix_Nimblegen2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrix_Nimblegen2.s2<-data.matrix_Nimblegen2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_nbl_stat<-tclArray()
			for(i in 0:dim(data.matrix_Nimblegen2.s2)[1]){ for(j in 0:dim(data.matrix_Nimblegen2.s2)[2]){ 
				if(i==0){ ta_nbl_stat[[i,j]]<-colnames(data.matrix_Nimblegen2.s2)[j] } else { 
				if(j==0){ ta_nbl_stat[[i,j]]<-rownames(data.matrix_Nimblegen2.s2)[i] } else {
				tem<-data.matrix_Nimblegen2.s2[i,j]
				ta_nbl_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrix_Nimblegen2.s3[[ts_val]]<<-data.matrix_Nimblegen2.s2			
			ta_nbl_stat2[[ts_val]]<<-ta_nbl_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Series-Matrix"){
			data.matrixNorm.m<-data.matrixNorm.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
			rsd<-rowSds(data.matrixNorm.m)
			i<-rsd>=std
			dat.f<-data.matrixNorm.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_S[[ts_val]]<<-fit2
			data.matrixNorm.f<-fit2
			ps1<-as.data.frame(data.matrixNorm.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrixNorm.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_smt_filt<-tclArray()
			for(i in 0:dim(data.matrixNorm.f2)[1]){ for(j in 0:dim(data.matrixNorm.f2)[2]){ 
				if(i==0){ ta_smt_filt[[i,j]]<-colnames(data.matrixNorm.f2)[j] } else { 
				if(j==0){ ta_smt_filt[[i,j]]<-rownames(data.matrixNorm.f2)[i] } else {
				tem<-data.matrixNorm.f2[i,j]
				ta_smt_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrixNorm.f3[[ts_val]]<<-data.matrixNorm.f2
			ta_smt_filt2[[ts_val]]<<-ta_smt_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrixNorm.f)!=0){
				err<-try({
					ttx<-topTable(data.matrixNorm.f,number=nrow(data.matrixNorm.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrixNorm.m)==TRUE)]
					data.matrixNorm.s<-data.matrixNorm.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrixNorm.f,number=nrow(data.matrixNorm.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrixNorm.m)==TRUE)])
					data.matrixNorm.s<-data.matrixNorm.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrixNorm.s2<-data.matrixNorm.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_smt_stat<-tclArray()
			for(i in 0:dim(data.matrixNorm.s2)[1]){ for(j in 0:dim(data.matrixNorm.s2)[2]){ 
				if(i==0){ ta_smt_stat[[i,j]]<-colnames(data.matrixNorm.s2)[j] } else { 
				if(j==0){ ta_smt_stat[[i,j]]<-rownames(data.matrixNorm.s2)[i] } else {
				tem<-data.matrixNorm.s2[i,j]
				ta_smt_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrixNorm.s3[[ts_val]]<<-data.matrixNorm.s2			
			ta_smt_stat2[[ts_val]]<<-ta_smt_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Online-Data"){
			data.matrix_onlineNorm.m<-data.matrix_onlineNorm.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
			rsd<-rowSds(data.matrix_onlineNorm.m)
			i<-rsd>=std
			dat.f<-data.matrix_onlineNorm.m[i,]
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_O[[ts_val]]<<-fit2
			data.matrix_onlineNorm.f<-fit2
			ps1<-as.data.frame(data.matrix_onlineNorm.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrix_onlineNorm.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_onl_filt<-tclArray()
			for(i in 0:dim(data.matrix_onlineNorm.f2)[1]){ for(j in 0:dim(data.matrix_onlineNorm.f2)[2]){ 
				if(i==0){ ta_onl_filt[[i,j]]<-colnames(data.matrix_onlineNorm.f2)[j] } else { 
				if(j==0){ ta_onl_filt[[i,j]]<-rownames(data.matrix_onlineNorm.f2)[i] } else {
				tem<-data.matrix_onlineNorm.f2[i,j]
				ta_onl_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrix_onlineNorm.f3[[ts_val]]<<-data.matrix_onlineNorm.f2
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			ta_onl_filt2[[ts_val]]<<-ta_onl_filt
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrix_onlineNorm.f)!=0){
				err<-try({
					ttx<-topTable(data.matrix_onlineNorm.f,number=nrow(data.matrix_onlineNorm.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_onlineNorm.m)==TRUE)]
					data.matrix_onlineNorm.s<-data.matrix_onlineNorm.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrix_onlineNorm.f,number=nrow(data.matrix_onlineNorm.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_onlineNorm.m)==TRUE)])
					data.matrix_onlineNorm.s<-data.matrix_onlineNorm.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrix_onlineNorm.s2[[ts_val]]<-data.matrix_onlineNorm.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_onl_stat[[ts_val]]<-tclArray()
			for(i in 0:dim(data.matrix_onlineNorm.s2)[1]){ for(j in 0:dim(data.matrix_onlineNorm.s2)[2]){ 
				if(i==0){ ta_onl_stat[[i,j]]<-colnames(data.matrix_onlineNorm.s2)[j] } else { 
				if(j==0){ ta_onl_stat[[i,j]]<-rownames(data.matrix_onlineNorm.s2)[i] } else {
				tem<-data.matrix_onlineNorm.s2[i,j]
				ta_onl_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrix_onlineNorm.s3[[ts_val]]<<-data.matrix_onlineNorm.s2			
			ta_onl_stat2[[ts_val]]<<-ta_onl_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
	}

	exprs_filt<-function(h,h2,h3,h4,h5,h6,...){
		ts_name=h;ts_val=h2;children<-h3;r_choice=h4;ove<-as.numeric(h5);posp<-as.numeric(h6);
		if(ts_name=="Affymetrix"){
			dat2Affy.m<-dat2Affy.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(dat2Affy.m,fff)
			dat.fo<-dat2Affy.m[i,]
			i<-genefilter(-dat2Affy.m,fff)
			dat.fu<-dat2Affy.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Affy[[ts_val]]<<-fit2
			dat2Affy.f<-fit2
			ps1<-as.data.frame(dat2Affy.f)	
			rownames(ps1)<-rownames(fit2)
			dat2Affy.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_affy_filt<-tclArray()
			for(i in 0:dim(dat2Affy.f2)[1]){ for(j in 0:dim(dat2Affy.f2)[2]){ 
				if(i==0){ ta_affy_filt[[i,j]]<-colnames(dat2Affy.f2)[j] } else { 
				if(j==0){ ta_affy_filt[[i,j]]<-rownames(dat2Affy.f2)[i] } else {
				tem<-dat2Affy.f2[i,j]
				ta_affy_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			dat2Affy.f3[[ts_val]]<<-dat2Affy.f2
			ta_affy_filt2[[ts_val]]<<-ta_affy_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(dat2Affy.f)!=0){
				err<-try({
					ttx<-topTable(dat2Affy.f,number=nrow(dat2Affy.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(dat2Affy.m)==TRUE)]
					dat2Affy.s<-dat2Affy.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(dat2Affy.f,number=nrow(dat2Affy.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(dat2Affy.m)==TRUE)])
					dat2Affy.s<-dat2Affy.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			dat2Affy.s2<-dat2Affy.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_affy_stat<-tclArray()
			for(i in 0:dim(dat2Affy.s2)[1]){ for(j in 0:dim(dat2Affy.s2)[2]){ 
				if(i==0){ ta_affy_stat[[i,j]]<-colnames(dat2Affy.s2)[j] } else { 
				if(j==0){ ta_affy_stat[[i,j]]<-rownames(dat2Affy.s2)[i] } else {
				tem<-dat2Affy.s2[i,j]
				ta_affy_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			dat2Affy.s3[[ts_val]]<<-dat2Affy.s2			
			ta_affy_stat2[[ts_val]]<<-ta_affy_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Agilent-OneColor"){
			datAgOne2.m<-datAgOne2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(datAgOne2.m,fff)
			dat.fo<-datAgOne2.m[i,]
			i<-genefilter(-datAgOne2.m,fff)
			dat.fu<-datAgOne2.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Ag1[[ts_val]]<<-fit2
			datAgOne2.f<-fit2
			ps1<-as.data.frame(datAgOne2.f)	
			rownames(ps1)<-rownames(fit2)
			datAgOne2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ag1_filt<-tclArray()
			for(i in 0:dim(datAgOne2.f2)[1]){ for(j in 0:dim(datAgOne2.f2)[2]){ 
				if(i==0){ ta_ag1_filt[[i,j]]<-colnames(datAgOne2.f2)[j] } else { 
				if(j==0){ ta_ag1_filt[[i,j]]<-rownames(datAgOne2.f2)[i] } else {
				tem<-datAgOne2.f2[i,j]
				ta_ag1_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datAgOne2.f3[[ts_val]]<<-datAgOne2.f2
			ta_ag1_filt2[[ts_val]]<<-ta_ag1_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datAgOne2.f)!=0){
				err<-try({
					ttx<-topTable(datAgOne2.f,number=nrow(datAgOne2.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgOne2.m)==TRUE)]
					datAgOne2.s<-datAgOne2.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datAgOne2.f,number=nrow(datAgOne2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgOne2.m)==TRUE)])
					datAgOne2.s<-datAgOne2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datAgOne2.s2<-datAgOne2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ag1_stat<-tclArray()
			for(i in 0:dim(datAgOne2.s2)[1]){ for(j in 0:dim(datAgOne2.s2)[2]){ 
				if(i==0){ ta_ag1_stat[[i,j]]<-colnames(datAgOne2.s2)[j] } else { 
				if(j==0){ ta_ag1_stat[[i,j]]<-rownames(datAgOne2.s2)[i] } else {
				tem<-datAgOne2.s2[i,j]
				ta_ag1_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datAgOne2.s3[[ts_val]]<<-datAgOne2.s2			
			ta_ag1_stat2[[ts_val]]<<-ta_ag1_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Agilent-TwoColor"){
			datAgTwo2.m<-datAgTwo2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(datAgTwo2.m,fff)
			dat.fo<-datAgTwo2.m[i,]
			i<-genefilter(-datAgTwo2.m,fff)
			dat.fu<-datAgTwo2.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Ag2[[ts_val]]<<-fit2
			datAgTwo2.f<-fit2
			ps1<-as.data.frame(datAgTwo2.f)	
			rownames(ps1)<-rownames(fit2)
			datAgTwo2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ag2_filt<-tclArray()
			for(i in 0:dim(datAgTwo2.f2)[1]){ for(j in 0:dim(datAgTwo2.f2)[2]){ 
				if(i==0){ ta_ag2_filt[[i,j]]<-colnames(datAgTwo2.f2)[j] } else { 
				if(j==0){ ta_ag2_filt[[i,j]]<-rownames(datAgTwo2.f2)[i] } else {
				tem<-datAgTwo2.f2[i,j]
				ta_ag2_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datAgTwo2.f3[[ts_val]]<<-datAgTwo2.f2
			ta_ag2_filt2[[ts_val]]<<-ta_ag2_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datAgTwo2.f)!=0){
				err<-try({
						ttx<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)]
						datAgTwo2.s<-datAgTwo2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)])
					datAgTwo2.s<-datAgTwo2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datAgTwo2.s2<-datAgTwo2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ag2_stat<-tclArray()
			for(i in 0:dim(datAgTwo2.s2)[1]){ for(j in 0:dim(datAgTwo2.s2)[2]){ 
				if(i==0){ ta_ag2_stat[[i,j]]<-colnames(datAgTwo2.s2)[j] } else { 
				if(j==0){ ta_ag2_stat[[i,j]]<-rownames(datAgTwo2.s2)[i] } else {
				tem<-datAgTwo2.s2[i,j]
				ta_ag2_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datAgTwo2.s3[[ts_val]]<<-datAgTwo2.s2			
			ta_ag2_stat2[[ts_val]]<<-ta_ag2_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Illumina-Beadarray"){
			datIllBA2.m<-datIllBA2.m2[[ts_val]]		
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(datIllBA2.m,fff)
			dat.fo<-datIllBA2.m[i,]
			i<-genefilter(-datIllBA2.m,fff)
			dat.fu<-datIllBA2.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Il_B[[ts_val]]<<-fit2
			datIllBA2.f<-fit2
			ps1<-as.data.frame(datIllBA2.f)	
			rownames(ps1)<-rownames(fit2)
			datIllBA2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ilb_filt<-tclArray()
			for(i in 0:dim(datIllBA2.f2)[1]){ for(j in 0:dim(datIllBA2.f2)[2]){ 
				if(i==0){ ta_ilb_filt[[i,j]]<-colnames(datIllBA2.f2)[j] } else { 
				if(j==0){ ta_ilb_filt[[i,j]]<-rownames(datIllBA2.f2)[i] } else {
				tem<-datIllBA2.f2[i,j]
				ta_ilb_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			datIllBA2.f3[[ts_val]]<<-datIllBA2.f2
			ta_ilb_filt2[[ts_val]]<<-ta_ilb_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(datIllBA2.f)!=0){
				err<-try({
						ttx<-topTable(datIllBA2.f,number=nrow(datIllBA2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datIllBA2.m1)==TRUE)]
						datIllBA2.s<-datIllBA2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(datIllBA2.f,number=nrow(datIllBA2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datIllBA2.m1)==TRUE)])
					datIllBA2.s<-datIllBA2.m1[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			datIllBA2.s2<-datIllBA2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ilb_stat<-tclArray()
			for(i in 0:dim(datIllBA2.s2)[1]){ for(j in 0:dim(datIllBA2.s2)[2]){ 
				if(i==0){ ta_ilb_stat[[i,j]]<-colnames(datIllBA2.s2)[j] } else { 
				if(j==0){ ta_ilb_stat[[i,j]]<-rownames(datIllBA2.s2)[i] } else {
				tem<-datIllBA2.s2[i,j]
				ta_ilb_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			datIllBA2.s3[[ts_val]]<<-datIllBA2.s2			
			ta_ilb_stat2[[ts_val]]<<-ta_ilb_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Illumina-Lumi"){
			lumi_NQ.m<-lumi_NQ.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(lumi_NQ.m,fff)
			dat.fo<-lumi_NQ.m[i,]
			i<-genefilter(-lumi_NQ.m,fff)
			dat.fu<-lumi_NQ.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_Il_L[[ts_val]]<<-fit2
			lumi_NQ.f<-fit2
			ps1<-as.data.frame(lumi_NQ.f)	
			rownames(ps1)<-rownames(fit2)
			lumi_NQ.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_ill_filt<-tclArray()
			for(i in 0:dim(lumi_NQ.f2)[1]){ for(j in 0:dim(lumi_NQ.f2)[2]){ 
				if(i==0){ ta_ill_filt[[i,j]]<-colnames(lumi_NQ.f2)[j] } else { 
				if(j==0){ ta_ill_filt[[i,j]]<-rownames(lumi_NQ.f2)[i] } else {
				tem<-lumi_NQ.f2[i,j]
				ta_ill_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			lumi_NQ.f3[[ts_val]]<<-lumi_NQ.f2
			ta_ill_filt2[[ts_val]]<<-ta_ill_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(lumi_NQ.f)!=0){
				err<-try({
						ttx<-topTable(lumi_NQ.f,number=nrow(lumi_NQ.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(lumi_NQ.m)==TRUE)]
						lumi_NQ.s<-lumi_NQ.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(lumi_NQ.f,number=nrow(lumi_NQ.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(lumi_NQ.m)==TRUE)])
					lumi_NQ.s<-lumi_NQ.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			lumi_NQ.s2<-lumi_NQ.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_ill_stat<-tclArray()
			for(i in 0:dim(lumi_NQ.s2)[1]){ for(j in 0:dim(lumi_NQ.s2)[2]){ 
				if(i==0){ ta_ill_stat[[i,j]]<-colnames(lumi_NQ.s2)[j] } else { 
				if(j==0){ ta_ill_stat[[i,j]]<-rownames(lumi_NQ.s2)[i] } else {
				tem<-lumi_NQ.s2[i,j]
				ta_ill_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			lumi_NQ.s3[[ts_val]]<<-lumi_NQ.s2			
			ta_ill_stat2[[ts_val]]<<-ta_ill_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Nimblegen"){
			data.matrix_Nimblegen2.m<-data.matrix_Nimblegen2.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(data.matrix_Nimblegen2.m,fff)
			dat.fo<-data.matrix_Nimblegen2.m[i,]
			i<-genefilter(-data.matrix_Nimblegen2.m,fff)
			dat.fu<-data.matrix_Nimblegen2.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_N[[ts_val]]<<-fit2
			data.matrix_Nimblegen2.f<-fit2
			ps1<-as.data.frame(data.matrix_Nimblegen2.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrix_Nimblegen2.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_nbl_filt<-tclArray()
			for(i in 0:dim(data.matrix_Nimblegen2.f2)[1]){ for(j in 0:dim(data.matrix_Nimblegen2.f2)[2]){ 
				if(i==0){ ta_nbl_filt[[i,j]]<-colnames(data.matrix_Nimblegen2.f2)[j] } else { 
				if(j==0){ ta_nbl_filt[[i,j]]<-rownames(data.matrix_Nimblegen2.f2)[i] } else {
				tem<-data.matrix_Nimblegen2.f2[i,j]
				ta_nbl_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrix_Nimblegen2.f3[[ts_val]]<<-data.matrix_Nimblegen2.f2
			ta_nbl_filt2[[ts_val]]<<-ta_nbl_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrix_Nimblegen2.f)!=0){
				err<-try({
						ttx<-topTable(data.matrix_Nimblegen2.f,number=nrow(data.matrix_Nimblegen2.m))
						rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_Nimblegen2.m)==TRUE)]
						data.matrix_Nimblegen2.s<-data.matrix_Nimblegen2.m[rn,]
					},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrix_Nimblegen2.f,number=nrow(data.matrix_Nimblegen2.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_Nimblegen2.m)==TRUE)])
					data.matrix_Nimblegen2.s<-data.matrix_Nimblegen2.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrix_Nimblegen2.s2<-data.matrix_Nimblegen2.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_nbl_stat<-tclArray()
			for(i in 0:dim(data.matrix_Nimblegen2.s2)[1]){ for(j in 0:dim(data.matrix_Nimblegen2.s2)[2]){ 
				if(i==0){ ta_nbl_stat[[i,j]]<-colnames(data.matrix_Nimblegen2.s2)[j] } else { 
				if(j==0){ ta_nbl_stat[[i,j]]<-rownames(data.matrix_Nimblegen2.s2)[i] } else {
				tem<-data.matrix_Nimblegen2.s2[i,j]
				ta_nbl_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrix_Nimblegen2.s3[[ts_val]]<<-data.matrix_Nimblegen2.s2			
			ta_nbl_stat2[[ts_val]]<<-ta_nbl_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Series-Matrix"){
			data.matrixNorm.m<-data.matrixNorm.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(data.matrixNorm.m,fff)
			dat.fo<-data.matrixNorm.m[i,]
			i<-genefilter(-data.matrixNorm.m,fff)
			dat.fu<-data.matrixNorm.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_S[[ts_val]]<<-fit2
			data.matrixNorm.f<-fit2
			ps1<-as.data.frame(data.matrixNorm.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrixNorm.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_smt_filt<-tclArray()
			for(i in 0:dim(data.matrixNorm.f2)[1]){ for(j in 0:dim(data.matrixNorm.f2)[2]){ 
				if(i==0){ ta_smt_filt[[i,j]]<-colnames(data.matrixNorm.f2)[j] } else { 
				if(j==0){ ta_smt_filt[[i,j]]<-rownames(data.matrixNorm.f2)[i] } else {
				tem<-data.matrixNorm.f2[i,j]
				ta_smt_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrixNorm.f3[[ts_val]]<<-data.matrixNorm.f2
			ta_smt_filt2[[ts_val]]<<-ta_smt_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrixNorm.f)!=0){
				err<-try({
					ttx<-topTable(data.matrixNorm.f,number=nrow(data.matrixNorm.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrixNorm.m)==TRUE)]
					data.matrixNorm.s<-data.matrixNorm.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrixNorm.f,number=nrow(data.matrixNorm.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrixNorm.m)==TRUE)])
					data.matrixNorm.s<-data.matrixNorm.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrixNorm.s2<-data.matrixNorm.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_smt_stat<-tclArray()
			for(i in 0:dim(data.matrixNorm.s2)[1]){ for(j in 0:dim(data.matrixNorm.s2)[2]){ 
				if(i==0){ ta_smt_stat[[i,j]]<-colnames(data.matrixNorm.s2)[j] } else { 
				if(j==0){ ta_smt_stat[[i,j]]<-rownames(data.matrixNorm.s2)[i] } else {
				tem<-data.matrixNorm.s2[i,j]
				ta_smt_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrixNorm.s3[[ts_val]]<<-data.matrixNorm.s2			
			ta_smt_stat2[[ts_val]]<<-ta_smt_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
		if(ts_name=="Online-Data"){
			data.matrix_onlineNorm.m<-data.matrix_onlineNorm.m2[[ts_val]]
pb_ma<-tkProgressBar(title="Filtering...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
			fff<-pOverA(A=ove,p=posp)
			i<-genefilter(data.matrix_onlineNorm.m,fff)
			dat.fo<-data.matrix_onlineNorm.m[i,]
			i<-genefilter(-data.matrix_onlineNorm.m,fff)
			dat.fu<-data.matrix_onlineNorm.m[i,]
			dat.f<-unique(rbind(dat.fo,dat.fu))
			fit<-lmFit(dat.f)
			fit2<-eBayes(fit)
			fit2_O[[ts_val]]<<-fit2
			data.matrix_onlineNorm.f<-fit2
			ps1<-as.data.frame(data.matrix_onlineNorm.f)	
			rownames(ps1)<-rownames(fit2)
			data.matrix_onlineNorm.f2<-ps1
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
			ta_onl_filt<-tclArray()
			for(i in 0:dim(data.matrix_onlineNorm.f2)[1]){ for(j in 0:dim(data.matrix_onlineNorm.f2)[2]){ 
				if(i==0){ ta_onl_filt[[i,j]]<-colnames(data.matrix_onlineNorm.f2)[j] } else { 
				if(j==0){ ta_onl_filt[[i,j]]<-rownames(data.matrix_onlineNorm.f2)[i] } else {
				tem<-data.matrix_onlineNorm.f2[i,j]
				ta_onl_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }
			data.matrix_onlineNorm.f3[[ts_val]]<<-data.matrix_onlineNorm.f2
			ta_onl_filt2[[ts_val]]<<-ta_onl_filt
setTkProgressBar(pb_ma,0.6,title="Statistical_Significant...",label="")
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Filtering"))
			}
			if(length(data.matrix_onlineNorm.f)!=0){
				err<-try({
					ttx<-topTable(data.matrix_onlineNorm.f,number=nrow(data.matrix_onlineNorm.m))
					rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_onlineNorm.m)==TRUE)]
					data.matrix_onlineNorm.s<-data.matrix_onlineNorm.m[rn,]
				},silent=TRUE)
				if(length(grep("Error",err))!=0)
				{
					ttx<-topTable(data.matrix_onlineNorm.f,number=nrow(data.matrix_onlineNorm.m))
					rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(data.matrix_onlineNorm.m)==TRUE)])
					data.matrix_onlineNorm.s<-data.matrix_onlineNorm.m[rownames(ttx)[ttx$P.Value<=0.01],]
				}
			}
			data.matrix_onlineNorm.s2<-data.matrix_onlineNorm.s
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
			ta_onl_stat<-tclArray()
			for(i in 0:dim(data.matrix_onlineNorm.s2)[1]){ for(j in 0:dim(data.matrix_onlineNorm.s2)[2]){ 
				if(i==0){ ta_onl_stat[[i,j]]<-colnames(data.matrix_onlineNorm.s2)[j] } else { 
				if(j==0){ ta_onl_stat[[i,j]]<-rownames(data.matrix_onlineNorm.s2)[i] } else {
				tem<-data.matrix_onlineNorm.s2[i,j]
				ta_onl_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
				} }
			} }			
			data.matrix_onlineNorm.s3[[ts_val]]<<-data.matrix_onlineNorm.s2			
			ta_onl_stat2[[ts_val]]<<-ta_onl_stat
setTkProgressBar(pb_ma,1,title="Completed...",label="")	
close(pb_ma)
			for(i in 1:length(children)){
				x<-as.character(tcl(treeview,"item",children[i],"-values"))
				if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...Statistical_Significant"))
			}
		}
	}

	filter_params<-function(h,h2,h3,h4,...){
		ts_name<-h;ts_val<-h2;children<-h3;r_choice=h4
		w_imp2<-tktoplevel()
		tkwm.title(w_imp2,"Select a filter")
		tkwm.resizable(w_imp2,0,0)
		frame1_imp2<-ttkframe(w_imp2,padding=c(3,3,12,12))
		tkpack(frame1_imp2,expand=TRUE,fill="both",side="top")
		r1_imp2<-c("Standard Deviation","Expression")
		var1<-tclVar(r1_imp2[1])
		sapply(r1_imp2,function(i){
			r1_imp2_vals<-ttkradiobutton(frame1_imp2,variable=var1,text=i,value=i)
			tkpack(r1_imp2_vals,side="left",anchor="w",padx=45)
		})
		frame2_imp2<-ttkframe(w_imp2,padding=c(3,3,12,12),height=30,width=50,borderwidth=1,relief="groove")
		tkpack(frame2_imp2,expand=TRUE,fill="both",side="left")
		frame3_imp2<-ttkframe(w_imp2,padding=c(3,3,12,12),height=30,width=50,borderwidth=1,relief="groove")
		tkpack(frame3_imp2,expand=TRUE,fill="both",side="left")
		frame4_imp2<-ttkframe(w_imp2,padding=c(3,3,12,12),height=30,width=50,borderwidth=1,relief="groove")
		tkpack(frame4_imp2,expand=TRUE,fill="both",side="left")
		tkpack(ttklabel(frame2_imp2,text='Standard Deviation value'),side="top",padx=0)
		std_value<-tclVar("")
		tkpack(ttkentry(frame2_imp2,textvariable=std_value,width=25),side="top",anchor="e")
		tkpack(ttklabel(frame3_imp2,text='Over Expression Value'),side="top",padx=0)
		exp_value<-tclVar("")
		tkpack(ttkentry(frame3_imp2,textvariable=exp_value,width=25),side="top",anchor="e")
		tkpack(ttklabel(frame3_imp2,text='Percentage of Samples'),side="top",padx=0)
		prcnt<-tclVar("")
		tkpack(ttkentry(frame3_imp2,textvariable=prcnt,width=25),side="top",anchor="e")
		r_but<-ttkbutton(frame4_imp2,text="Ok")
		tkpack(r_but,side="top")
		tkconfigure(r_but,command=function(){
			tkwm.withdraw(w_imp2)
			if(tclvalue(var1)=="Standard Deviation"){ stdev_filt(ts_name,ts_val,children,r_choice,tclvalue(std_value)) }
			if(tclvalue(var1)=="Expression"){ exprs_filt(ts_name,ts_val,children,r_choice,tclvalue(exp_value),tclvalue(prcnt)) }
		})
	}		

	r_choice="._."
	children<-as.character(tcl(treeview,"children",""))
	w_analz<-tktoplevel()
	w_analz_frame<-ttkframe(w_analz,padding=c(3,3,50,20),borderwidth=1,relief="groove")
	tkpack(w_analz_frame,expand=TRUE,fill="both",side="left")
	var<-tclVar(tree_prnts[1])
	sapply(tree_prnts,function(i){
		r_but_vals<-ttkradiobutton(w_analz_frame,variable=var,text=i,value=i)
		tkpack(r_but_vals,side="top",anchor="w")
	})
	tkpack(ttklabel(w_analz_frame,text=''))
	tkpack(ttklabel(w_analz_frame,text=''))
	r_but<-ttkbutton(w_analz_frame,text="Ok")
	tkpack(r_but,pady=2)
	tkconfigure(r_but,command=function(){
		r_choice<-tclvalue(var)
		tkwm.withdraw(w_analz)
		tree_slc<-strsplit(r_choice[1],"_")
		ts_name<-tree_slc[[1]][1]
		ts_val<-as.numeric(tree_slc[[1]][2])
		filter_params(ts_name,ts_val,children,r_choice)
	})
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,1,title="Done...",label="")				
close(pb_ma)
filter_unsp()