[BioC] Simple Affy

Jason Skelton jps at sanger.ac.uk
Wed Jun 30 11:33:25 CEST 2004

I'm asking this question on behalf of someone else so forgive the 
question as
i'm not at all familar with the affy or simpleaffy packages.

Using R 1.9.0
Affy 1.4.32
SimpleAffy 1.2.2

 > fake.raw <- read.affy(covdesc="covdescstrainsFake.txt")
 > fake.eset <- rma.newmalv2(fake.raw)
Setting environment to newmalv2cdf...
Background correction with rma...
Quantile normalisation...
Median polishing...
5460 ids to be processed

 > results.fake <- pairwise.comparison(fake.eset, "strain", 
Error in get.fold.change.and.t.test(x, group, members, logged = logged,  :
        a or b too big or not enough iterations in betacf

Apparently these commands worked OK with R version 1.8.1 etc..........
and older ? versions of simple affy 1.0.9 (developmental version)

Any ideas much appreciated
many thanks


Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919

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