Reading Microarray Data to R
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 :)
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siddharth.avadhanam •
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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).
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 ?