Hi everybody, I am working on 10 GPR files from a time course cDNA array experiment.Aftersome normalization steps,i got the M and A for 10 arrays.And then i want to apply the quality control procedures to flag logratio(M) for those spots to Na whose inteinsities form either channel is lower than 200.what can i do? The procedures i did are as follows: library(marray) file=c('2000009478.gpr','2000009471.gpr','2000009472.gpr','2000009473. gpr',' 2000009479.gpr','2000009466.gpr','2000009467.gpr','2000009468.gpr',' 2000009480.gpr','2000009481.gpr') target<-read.marrayInfo(fname="e:/gpr/zpz/zpz-target.txt") ##Read probe related information galinfo<-read.Galfile("GAL-13K.txt",path="e:/gpr/zpz") ##Read expression data zraw=read.GenePix (fnames=file,path="e:/gpr/zpz/results",layout=galinfo$layout,gnames=ga linfo$gnemes,target=target) ##normalization on print tips zraw.norm=maNormMain(zraw) ##Between slides normalization zraw.normg=maNormScale(zraw.norm,norm="g") ##And then the genefilter procedures, ## I want to flag the logratio(M) to NA according to the intensity of both channels of a spot,and then select the genes if the ### sbsolute logratio(|M|) is grater than one.What can i do,what's the code doing that? Thanks in advance. Shi Jiantao [[alternative HTML version deleted]]

On May 6, 2005, at 2:46 AM, Xiao Shi wrote: > Hi everybody, > I am working on 10 GPR files from a time course cDNA array > experiment.Aftersome normalization steps,i got the M and A for 10 > arrays.And then i want to apply the quality control procedures to flag > logratio(M) for those spots to Na whose inteinsities form either > channel is > lower than 200.what can i do? > > The procedures i did are as follows: > library(marray) > file=c('2000009478.gpr','2000009471.gpr','2000009472.gpr','200000947 3.g > pr',' > 2000009479.gpr','2000009466.gpr','2000009467.gpr','2000009468.gpr',' > 2000009480.gpr','2000009481.gpr') > target<-read.marrayInfo(fname="e:/gpr/zpz/zpz-target.txt") > ##Read probe related information > galinfo<-read.Galfile("GAL-13K.txt",path="e:/gpr/zpz") > ##Read expression data > zraw=read.GenePix > (fnames=file,path="e:/gpr/zpz/ > results",layout=galinfo$layout,gnames=galinfo$gnemes,target=target) > > ##normalization on print tips > zraw.norm=maNormMain(zraw) > > ##Between slides normalization > zraw.normg=maNormScale(zraw.norm,norm="g") > > ##And then the genefilter procedures, > ## I want to flag the logratio(M) to NA according to the intensity of > both > channels of a spot,and then select the genes if the > ### sbsolute logratio(|M|) is grater than one.What can i do,what's the > code > doing that? The better way to do this in the limma framework is to set the weight for the spot to some small number (or 0). A search of the bioconductor archives (here: http://files.protsuggest.org/cgi-bin/biocond.cgi) pulls up a couple of threads worth reading: http://files.protsuggest.org/biocond/html/4342.html http://files.protsuggest.org/biocond/html/3295.html However, if you STILL really want to set them to NA after reading some more, you can do that simply like: zraw.normrg$M[(zraw$R<200) | (zraw$G<200)] <- NA Sean Sean.