[Bioc-devel] medianpolish for Affymetrix genechip probesets

Wolfgang Huber huber at ebi.ac.uk
Fri Mar 9 15:31:40 CET 2007

Hi Rafa, Ben et al.,

what is nowadays the prefered implementation of the "medianpolish" 
probeset summarization / expression value computation method, and which 
interface to it do you recommend others to use?

I have just been looking through affy, BufferedMatrixMethods, oligo, 
affyPLM, gcrma and found the choice exciting, stimulating and ... large.

The reason for the question: vsn can be used to do bg correction and 
normalization of Affy genechips together with medianpolish to summarize. 
In the vsn vignette I have so far been recommending to use

expresso(x, bg.correct=FALSE, normalize.method="vsn",
          pmcorrect.method="pmonly", summary.method="medianpolish")

but this can be very slow and I would like to provide a more efficient 
wrapper à la rma() without reinventing the medianpolish wheel.

So far I gather that

1. I should use, in affy/src/rma2.c:
SEXP rma_c_call(SEXP PMmat, SEXP MMmat, SEXP ProbeNamesVec,
                 SEXP N_probes, SEXP norm_flag)
with norm_flag==0, and

2. that I need to exponentiate (2^x) the vsn-transformed data before 
sending it that way because the first thing you do there is to take log2.

Is this correct? Any pointers or comments are welcome.

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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