I used the following code lines to read in Agilent data within limma: targets=readTargets("C:/caimiao/two_channel_one_channel/target1.txt") > targets SlideNumber FileName Cy3 Cy5 5ugDay1s1 1 5ugDay1s1.txt Sample1 Uref 5ugDay1s2 2 5ugDay1s2.txt Sample1 Uref 5ugDay1s3 3 5ugDay1s3.txt Sample1 Uref 5ugDay1s4 4 5ugDay1s4.txt Uref Sample1 5ugDay1s5 5 5ugDay1s5.txt Uref Sample1 5ugDay1s6 6 5ugDay1s6.txt Uref Sample1 RG=read.maimages(files=targets$FileName, source="agilent", path="C:/caimiao/day1", names=NULL, columns=list(gene="ProbeName", col="Col", row="Row", Rf="rMeanSignal", Rb="gBGMeanSignal",Gf="gMeanSignal", Gb="gBGMeanSignal"), other.columns=list( col="Col", row= "Row", controltype="ControlType"), annotation=list (gene="ProbeName")) > RG$targets FileName 5ugDay1s1 5ugDay1s1.txt 5ugDay1s2 5ugDay1s2.txt 5ugDay1s3 5ugDay1s3.txt 5ugDay1s4 5ugDay1s4.txt 5ugDay1s5 5ugDay1s5.txt 5ugDay1s6 5ugDay1s6.txt What I don't understand is why the output for the command "RG$targets" does not have the Cy3 and Cy5 information? Thanks, Caimiao

Hi, read.maimages does not use information from the targets file in data uploading so it cannot know about the Cy3, Cy5 RNA labelling columns. If you look in the relevant code for read.maimage, the targets element in the RG list is written from the following line, RG$targets <- data.frame(FileName = I(files), row.names = names) These *are* only the filenames. If you want to update the targets element in the RG list then you could reassign the target informatino to the list element RG$targets. RG <-read.maimages(files=targets$FileName, source="agilent", path="C:/caimiao/day1", names=NULL, columns=list(gene="ProbeName", col="Col", row="Row", Rf="rMeanSignal", Rb="gBGMeanSignal",Gf="gMeanSignal", Gb="gBGMeanSignal"), other.columns=list( col="Col", row= "Row", controltype="ControlType"), annotation=list (gene="ProbeName")) targets <- readTargets("C:/caimiao/two_channel_one_channel/target1.txt") RG$targets <- targets marcus >>> "Caimiao Wei" <caimiaow@u.washington.edu> 17/11/2004 11:12:59 AM >>> I used the following code lines to read in Agilent data within limma: targets=readTargets("C:/caimiao/two_channel_one_channel/target1.txt") > targets SlideNumber FileName Cy3 Cy5 5ugDay1s1 1 5ugDay1s1.txt Sample1 Uref 5ugDay1s2 2 5ugDay1s2.txt Sample1 Uref 5ugDay1s3 3 5ugDay1s3.txt Sample1 Uref 5ugDay1s4 4 5ugDay1s4.txt Uref Sample1 5ugDay1s5 5 5ugDay1s5.txt Uref Sample1 5ugDay1s6 6 5ugDay1s6.txt Uref Sample1 RG=read.maimages(files=targets$FileName, source="agilent", path="C:/caimiao/day1", names=NULL, columns=list(gene="ProbeName", col="Col", row="Row", Rf="rMeanSignal", Rb="gBGMeanSignal",Gf="gMeanSignal", Gb="gBGMeanSignal"), other.columns=list( col="Col", row= "Row", controltype="ControlType"), annotation=list (gene="ProbeName")) > RG$targets FileName 5ugDay1s1 5ugDay1s1.txt 5ugDay1s2 5ugDay1s2.txt 5ugDay1s3 5ugDay1s3.txt 5ugDay1s4 5ugDay1s4.txt 5ugDay1s5 5ugDay1s5.txt 5ugDay1s6 5ugDay1s6.txt What I don't understand is why the output for the command "RG$targets" does not have the Cy3 and Cy5 information? Thanks, Caimiao _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}