Simple Affy
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Jason Skelton ▴ 510
@jason-skelton-135
Last seen 7.3 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
cdf affy simpleaffy cdf affy simpleaffy • 590 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
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}}
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