[BioC] RE: BioC] simpleaffy betacf error in 1.2.3

[Crispin Miller]

Hi,
Sorry for not replying earlier - I was away at a conference - I'll take
a look at it and get back to you - in the meantime try the version
(1.2.6) in the devl branch and see if that is any better?

Crispin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jan folia
Sent: 02 August 2004 20:21
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] RE: BioC] simpleaffy betacf error in 1.2.3


Hi, 

Wonder if anyone has input on this problem. I have quite a number of
genes having the same expression across replicates, which i assume may
cause difficulty in calculating std. error for pairwise.comp (t tests).
As i went through previous archives, i am under the impression the
version 1.2.3 should fix the problem.  Or is there more recent release
up there that goes around this error?

thanks.

J.

 

 

From:<j_grandifolia at yahoo.com>To:bioconductor at stat.math.ethz.chDate:Sun,
1 Aug 2004 18:22:22 -0700 (PDT)Subject:[BioC] simpleaffy betacf error in
1.2.3 Plain Text Attachment [ Download File | Save to my Yahoo!
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Hi:I would like some suggestion on how to go around thefollowing error
with simpleaffy:Using:R 1.9.0simpleaffy 1.2.3Code:rawdata <-
read.affy(covdesc="covdesc.txt")rma <- rma(rawdata)pw.ua <-
pairwise.comparison(x=rma, group="treatment",members=c("u", "a"))Error
in get.fold.change.and.t.test(x, group, members,logged = logged,  :
a or b too big or not enough iterations inbetacfI got this error
initially with a lower version (1.09)of simpleaffy, and then upgrade it
to 1.2.3, assuggested in one of the archived email. But the errordid not
go away. Any suggestions would be muchappreciated!Jan Folia


		
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