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@yahoo.com>To:bioconductor@stat.math.ethz.chDate:Su n, 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! Briefcase ] 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 --------------------------------- [[alternative HTML version deleted]]

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@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Jan folia Sent: 02 August 2004 20:21 To: bioconductor@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@yahoo.com>To:bioconductor@stat.math.ethz.chDate:Su n, 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! Briefcase ] 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 --------------------------------- [[alternative HTML version deleted]] _______________________________________________ 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}}