[Bioc-devel] medianpolish for Affymetrix genechip probesets

[Wolfgang Huber]

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

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