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

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 before...) 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... Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Jason Skelton Sent: 30 June 2004 10:33 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Simple Affy 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}