Hi there, Has the original issue now been fixed? e.g: exon.counts <- fitDispersionFunction(exon.counts) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm, disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced I'm using R 3.0.1 x86_64-pc-linux-gnu (64-bit) DEXSEQ_1.8.0 I've attached the csv of my test and controls. The dispersion function works when I change the control / test samples to 50/50%. Now I have ~25 tests and ~150 controls and I see the above error. Thanks in advance. Chris?

Hi there, Has the original issue now been fixed? e.g: exon.counts <- fitDispersionFunction(exon.counts) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm, disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced I'm using R 3.0.1 x86_64-pc-linux-gnu (64-bit) DEXSEQ_1.8.0 I've attached the csv of my test and controls. The dispersion function works when I change the control / test samples to 50/50%. Now I have ~25 tests and ~150 controls and I see the above error. Thanks in advance. Chris ?

Dear Chris Thank you for the follow-up! The most recent version of DEXSeq is here: http://www.bioconductor.org/packages/devel/bioc/html/DEXSeq.html right now it is 1.9.5. so best if you could test with that. I?m afraid the .csv you wanted to attach has not made it to the list (see http://www.bioconductor.org/help/mailing-list/posting-guide the section on attachments). In addition, please also provide the code that produces the ?issue?. Best wishes Wolfgang On 10 Feb 2014, at 14:47, Odhams, Christopher <chris.odhams at="" kcl.ac.uk=""> wrote: > Hi there, > > Has the original issue now been fixed? > > e.g: > > exon.counts <- fitDispersionFunction(exon.counts) > > Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : > missing value where TRUE/FALSE needed > In addition: Warning messages: > 1: In glmgam.fit(mm, disps[good], start = coefs) : > Too much damping - convergence tolerance not achievable > 2: In log(coefs/oldcoefs) : NaNs produced > > I'm using R 3.0.1 > x86_64-pc-linux-gnu (64-bit) > DEXSEQ_1.8.0 > > I've attached the csv of my test and controls. > > The dispersion function works when I change the control / test samples to 50/50%. Now I have ~25 tests and ~150 controls and I see the above error. > > Thanks in advance. > Chris? > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor