ays, “raw” files are so-called CEL files (a file format invented by Affymetrix) and “processed” data is normalized and quantified data, summarized at the probeset level.</p>
<p>At the end of the day, GEO has series identifiers (like GSE19486) and sample identiers (GSM486297). Note the GSE vs GSM in the same. A user is almost always interested in all the samples in a given series, so the starting point is the series identifier, also called the accession number.</p>
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