GEO Affymetrix microarray datasets: how are series matrix files obtained from CEL files?

Question

[Ld_60]

Hi everyone,

I am working with microarray data from the GEO repository. I am trying to understand how to obtain the feature-sample matrix format, which is represented by the directly available "series matrix" file in GEO, from the CEL files (Affymetrix platforms)?

For example, considering the GPL96 microarray platform (i.e. Affymetrix Human Genome U133A Array), in the series matrix file, the samples are described by 22,283 features. Is there any package/command which allows to obtain such matrix from the CEL files? I tried using the gcrma normalization command (Bioconductor) on the CEL files for a dataset, but I got a number of features which is around 12,000.

Also, I am confused as to whether these features are called probes or probe sets, as I've seen different designations from different people?

Thanks a lot for your help.

[Benn]

Did you try the GEOquery package in R?

[Ld_60]

Hi, thank you very much for your answer, I will check that out!