[BioC] questions on the ImaGene data using limma package

[Ming YI [Contr]]

Hi, Dear Gordon:

I tried to use limma to deal with ImaGene dataset I downloaded from 
ArrayExpress. I never deal with ImaGene data before and not familiar 
with ImaGene data format except knowing that the Cy5 and Cy3 signals 
are stored in two separate files for the same sample. I tried to read 
the data into limma and normalize them in the context of limma. and I 
keep running into issues and errors. and I wish you can help me with 
this regard:

I did attach a file (E-NCMF-8_sdrf.txt) that was download from 
ArrayExpress can be potentially used for making the target file, and 
also I attached two raw data files of the ImaGene dataset as 
examples. The thing bothering me is as followed:

Extract 3538  and Extract 3526 (see column "Extract Name" of 
E-NCMF-8_sdrf.txt file) , they do have one Cy5 and one matched Cy3 
files, so that's fine with me. but in particular, for "Extract 
reference pool of 61 HNSCC" (see E-NCMF-8_sdrf.txt file), there are 
multiple Cy3 and Cy5 for such samples, how should we incorporate that 
into the target file?

I intended to use the following code to deal with this ImaGene data

targets<-readTargets()
files<-targets[,c("FileNameCy3", "FileNameCy5")'
RG<-read.maimages(files, source="imagene")

but I need the right target file to start with particularly with the 
issue I mentioned above.

Also for normalization, the
RG<-backgroundCorrect(RG, method="normexp", offset=50) still 
appropiate for ImaGene data?

Thanks so much for your help!

Ming Yi
ABCC
P.O.Box B, Bldg 430
National Cancer Institute/SAIC-Frederick, Inc
Frederick,Maryland
USA