[BioC] questions on the ImaGene data using limma package
Ming YI [Contr]
myi at ncifcrf.gov
Wed Oct 29 22:30:09 CET 2008
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
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
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!
P.O.Box B, Bldg 430
National Cancer Institute/SAIC-Frederick, Inc
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