[BioC] normalizeByReference package for Affymetrix ChIP-chip data

JENNIFER JUDY jtoolan1 at gw.johnshopkins.edu
Fri May 22 18:15:20 CEST 2009


We are currently trying to apply the normalizeByReference package to Affymetrix ChIP-chip data for human and mouse samples. Specifically, I am looking for advice regarding the background parameters (are control samples sufficient in this case). Additionally, does anyone have advice on how to create a probeAnno object with Affy's bpmap files? 

Any help is much appreciated!

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