Hi,

If I want to replicate as close as possible (or exactly, is it possible?)
the steps of Affy's software using Bioconductor packages, from background
subtraction, normalization, summarization to finding differential gene
expression. What's the best way to go about doing that? I've never used
Affy's own software (I'm learning microarray processing through documents
for bioconductor itself), but I want to make sure I'm doing things right by
taking raw data from GEO and compare to author's own published result using
Affy's standard methods before I switch to GCRMA, quantile, and median
polish.

For data preprocessing, I notice that in Affy's package there are these
options:
mas for background methods
mas5 for normalization
mas for PM correct method
mas for summarization methods

So are these the steps I should take?

How about for differential gene comparison? Which package should I use? Any
pointer would be appreciated, thanks. :)

Timothy

	[[alternative HTML version deleted]]

