Thanks all of you for the information.

However, as I mentioned in my previous emails, some GEO data (eg. GSM72287)
has both the .CEL file and .EXP file, and I looked up their paper:
http://www.ncbi.nlm.nih.gov/sites/entrez
and the authors mentioned that they did put the processed data as .CEL and
the raw as .EXP.

I understand that I could first download the supplementary files manually
from the GEO website, then input them as R object. But unfortunately, I am
doing meta-analysis on cancer microarrays, so I would have to download 20 +
datasets manually for getting the raw data . So I just wonder, in case the
raw data is available in the GEO, is there any way I could parse that
directly to R ?(since some of those have both processed and raw, but once
parsed using the getGEO, only the processed is shown)

Thanks again for all the comments and suggestions.



On 7/3/07, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> 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
>



-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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