How to perform differential gene expression analysis from RMA and GCRMA normalized values?

Question

[teeteen]

I would like to perform differential gene expression analysis on the GSE31243 dataset but with provided both RMA and GCRMA normalized values (separately) for both the Gracilis and Semitendinosus muscles.

How can I read these values into R and then perform a differential gene expression analysis with it. Any tutorial would be great. Thank you in advance!

Answer 1

[Gordon Smyth]

The RMA and GCRMA methods were developed as part of the Bioconductor project and Bioconductor provides many examples and tutorials of DE analysis for Affymetrix arrays. The Bioconductor project has a support site where you can ask for help:

https://support.bioconductor.org