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

James W. MacDonald jmacdon at med.umich.edu
Thu Apr 23 14:42:53 CEST 2009

Hi Jose,

J.delasHeras at ed.ac.uk wrote:
> Hi Jim,
> normalisation is not an issue, it's more to do with the summarisation of 
> probesets and something like 'Expresso' seems like a good way to do what 
> I need (and some other things I don't need).
> I am dealing with Nimblegen arrays. Both two colour (whole genome 
> promoter arrays, with anything up to 20 probes per probeset), and one 
> colour "a la Affymetrix" (expression arrays, with anything between 3 to 
> 8 probes per probeset).
> I've been dealing with teh two colour stuff just like I used to deal 
> with my spotted cDNA arrays, using Limma. To summarise the data... I've 
> used several approaches. Mostly I am not interested in the whole 2.7kb 
> that each "promoter region" comprises, so I've taken subsets blah 
> blah... Anyway, I'm happy with the results there.
> But for the expression data, I have one channel data, just like Affy 
> data. Numblegen provides already normalised and summarised data along 
> with the raw data, and they state they use the RMA procedure which I've 
> come across with when readingabout Affy chips, although I've never 
> analysed Affy data myself.
> I'm reasonably happy with the data given to me. It looks reasonable. So 
> I want to be able to do that myself rather than depending on their data 
> (thus allowing me to do things a bit differently if I want to), and 
> since the RMA-processed data looks good, I am interested in finding a 
> way to do RMA myself.
> You're right, the problem with my trying to make an AffyBatch from non 
> Affy data is that I'm going to have to create a cdf-like file... and 
> probably will encounter other obstacles... that's why I thought I'd ask 
> here, as there's people who are very familiar with that structure...
> In my naivety, it seems it should be a simple enough task... and as I'm 
> using 4 types of arrays mostly... I'd only have to do some work to make 
> these work and then just enjoy the ride as new experiments roll in...
> Am I naive? ;-)

Nope. Just looking in the wrong place. If you want to analyze Nimblegen 
single color data, then you need to use the oligo package rather than affy.

What package works for which type of oligonucleotide array can be found 




> I hope I clarified enough what I'm after.
> 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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