Question: Reading Microarray Data to R
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gravatar for siddharth.avadhanam
4.1 years ago by
India
siddharth.avadhanam30 wrote:

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     Viewer  Values 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 :) 

R • 1.3k views
ADD COMMENTlink written 4.1 years ago by siddharth.avadhanam30

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).

ADD REPLYlink written 4.1 years ago by Devon Ryan90k

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 ? 

 

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by siddharth.avadhanam30
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