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Jason Skelton
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510
@jason-skelton-135
Last seen 10.3 years ago
Hi
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",
c("wild","ref"))
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.
--
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA
Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919