GCRMA normalization from data frame

Question

[druggable]

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.

[Kevin Blighe]

CEL files not available?

Answer 1

[Gordon Smyth]

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.