[BioC] GEOquery on rawdata and processed data ?
sdavis2 at mail.nih.gov
Tue Jul 3 22:06:24 CEST 2007
Hi, Alex. The typical process would be to use getGEO to get a GSE or
GSEMatrix file and parse it into R. The data in these files are taken
directly from submitters to GEO and so could be processed by RMA, MAS5,
or any of several other methods. One will often need to refer to the
protocol information in GEO or to the associated paper to determine the
exact methods. As Saroj pointed out, in many cases, there is a link in
the GSE file or online on the summary page to supplementary files. This
link will, for Affy, usually contain at least .CEL files. One can then
use the getGEO function to get the processed data and annotation, then
get the raw .CEL files and process them however necessary, and replace
the values that come from GEO with the ones derived locally.
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