[BioC] GEOquery on rawdata and processed data ?

[Sean Davis]

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. 

Sean