Hi everyone,

I am analyzing a Affymetrix microarray data set using the Limma package. According to my experimental design, I understand that my contrasts are closely related and that I should use the "global" method for multiple testing. My question is: Is there a way to obtain P-values using the "global" method for multiple testing? The decideTest function allows to specify the method "global" but just give the matrix of the results and not the P-values. And if I understood correctly, the topTable function does not allow to specify the method for multiple testing and uses the "separate" method as default. Comparing the decideTest matrices, I realize that the results of "separate" and "global" methods are slightly different and I am concerned that this difference may change the final interpretation of my study.

Thank you very much.

Best regards

Eduardo Ribeiro
PhD student
University of Florida


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