[BioC] Simple Affy

Crispin Miller CMiller at PICR.man.ac.uk
Wed Jun 30 11:46:14 CEST 2004

Hi Jason,
I've been updating simpleaffy - I'm in the process of getting the latest
version into the CVS repositories - so hopefully it'll be on the website
in the next day or two... The version you want to be using is 1.2.3 -
I'll post to this list when it appears...

I've worked on a few bugs, including:
 o  a memory allocation problem for some array types, 
 o  the betacf issue described below (this happens when all the
expression levels in a set are identical for a particular gene - the
ttest function now returns NaN instead of falling over as it did
 o QC function not knowing about certain arrays....

There's some details about how we tested the accuracy of the
implementations on our website at:

http://bioinf.picr.man.ac.uk/simpleaffy I've so far only been able to
try things on a Linux platform, for example...


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jason
Sent: 30 June 2004 10:33
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Simple Affy

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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