[BioC] Target file for Limma

[Caimiao Wei]

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