Dear Ioannis thank you for the feedback! This should not happen. Would you be able to send us: - the output of "sessionInfo()" and, if at all possible, - the R code to reproduce your problem and a copy of cdsFull (perhaps with anonymized gene names if that's a consideration for you). One observation is that your size factors vary a lot (and this seems broadly to align with type a or b). If the data quality is very different for batches of the experiment, fitting the "type" effect in the GLM might not be enough to compensate for all the batch-related effects in your data, and perhaps separately normalising and testing the "a" and "b" samples, and then combining / overlapping the resulting gene lists or p-values might be more advisable ("meta-analysis"). Best wishes Wolfgang Il Jun/28/11 5:59 AM, ALok ha scritto: > Hi Ioannis > > Perhaps there is a 0 value, which is passed inside the function, needed to > compute some internal functions. It may explains lack of convergence in > glm.fit function. > I hope that this helps, > > Alok > > On Tue, Jun 28, 2011 at 12:18 AM, Filippis, Ioannis< > i.filippis at imperial.ac.uk> wrote: > >> Hi, >> >> I am trying to run fitNbinomGLMs but depending on the factor selected, it >> gives error "Error: NA/NaN/Inf in foreign function call (arg 1)". >> The counts matrix doesn't have any Na/NaN values, I cannot really >> understand what the problem is. I guess it shouldn't work for any factor if >> there was any problem with gene counts. >> >>> pData(cdsFull) >> sizeFactor condition type >> wtH1 2.17904027 treated a >> wtP1 0.24260614 treated b >> prH1 1.42343596 untreated a >> prP1 0.14120460 untreated b >> wtH4 3.45554434 treated a >> wtP4 2.38048956 treated b >> prH4 4.13642641 untreated a >> prP4 0.40209227 untreated b >> wtH7 3.76575182 treated a >> wtP7 0.88389937 treated b >> prH7 2.98917685 untreated a >> prP7 0.08601356 untreated b >>> head(counts(cdsFull)) >> wtH1 wtP1 prH1 prP1 wtH4 wtP4 prH4 prP4 wtH7 wtP7 prH7 prP7 >> 1 12 3 5 0 12 30 10 0 8 11 11 0 >> 2 195 14 99 0 14 31 38 2 36 12 39 1 >> 3 135 25 112 15 482 252 321 34 233 73 175 4 >> 4 149 11 119 22 525 181 828 92 998 181 1086 19 >> 5 6 0 8 0 5 3 3 0 2 0 12 0 >> 6 39 2 4 21 77 120 26 192 35 15 6 11 >> >>> fit0<-fitNbinomGLMs(cdsFull, count ~ type) >> ............. >> There were 26 warnings (use warnings() to see them) >>> fit1<-fitNbinomGLMs(cdsFull, count ~ condition) >> ..........Error: NA/NaN/Inf in foreign function call (arg 1) >> In addition: There were 21 warnings (use warnings() to see them) >>> fit1<-fitNbinomGLMs(cdsFull, count ~ condition + type) >> Error: NA/NaN/Inf in foreign function call (arg 1) >> In addition: Warning message: >> glm.fit: algorithm did not converge >> >> Many thanks for your help. >> >> Best, >> Ioannis >> _______________________________________________ >> 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 >> > > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber