Reading Microarray Data to R

Question

[siddharth.avadhanam]

Hi

I have a small concern regarding how R reads microarray data. I bring this up because the data for a microarray study that I can access through the accession viewer on the NCBI GEO database is completely different from what I get by downloading the .CEL files and reading them using the 'simpleaffy' package. I was wondering if I am doing something wrong, or if there is a better way to read this data using R ? For comparison I've pasted the values for the first 10 probe-dsids. ( second column is the accession viewer values, third column is the R values )

probes       Accession        Values
               Viewer       through R 
1007_s_at     4013.57        152
1053_at       231.8476       8313
117_at        46.92069       172
121_at        319.5398       8261
1255_g_at     27.49298       179
1294_at       184.4533       118
1316_at       126.9247       8182
1320_at       50.42599       166
1405_i_at     0.01327049     8257
1431_at       30.90967       152

Appreciate any help :)

[Devon Ryan]

Are the GEO values processed (probably)? If these happen to be V3 CEL files, then you can view them with less to ensure that the values in R match what's in the files (if they're not V3, you'll need to use a hex editor).

[siddharth.avadhanam]

These are not V3 CEL files. At least it doesn't say so on the accession viewer page. I think the difference may be that the values given in the data table on the website is processed data and the cel files that I download is raw data. In that case it would be better to work with the raw data right ?