[BioC] expresso: performing RMA on NON-Affy data?

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 22 17:16:33 CEST 2009

Hi Jose,

Do you want to do RMA, or just normalize? The problem with trying to 
wedge things into an AffyBatch is that the affy package will then try to 
find the cdfenv that contains the probe to probeset mappings, so by 
trying to leverage the AffyBatch infrastructure you will have to also 
come up with a fake cdf.

If you don't have probes that make up a probeset, then I'm not sure the 
affy package will be of use here.

Can you give more details?



J.delasHeras at ed.ac.uk wrote:
> Dear all,
> Is there a reasonable manner to coax expresso to normalise data that is 
> not Affymetrix?
> In other words, would it be possible[1] to create an AffyBatch manually, 
> filling the required slots with my own non-Affy data so that Expresso 
> can work on them?
> [1] possible it must be, but the effort required has to be conmensurate 
> with the results I'm after ;-)
> Any other alternative?
> Thank you.
> Jose

James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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