[BioC] Target file for Limma

[Marcus Davy]

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 at 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

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