GCRMA normalization from data frame
Hi Everyone,
I am analyzing multiple datasets from GEO, and I got the raw values. I need to perform GCRMA normalization, but this has to be from an AffyBatch object. Is there a way to directly perform gcrma or rma normalization directly on the data frame or matrix that I downloaded from GEO?
Many thanks.
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Gordon Smyth
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druggable •
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No, GCRMA normalization can only be performed on the complete data available from the Affymetrix CEL files.
Data matrices from GEO are already normalized anyway, so reapplying a normalization method would be inappropriate.
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CEL files not available?