Question: error in DEXSeq fitDispersionFunction()
0
gravatar for Wolfgang Huber
8.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Georg Thank you. Can you please try with a more recent version of DEXSeq, e.g. 1.1.1 from the last release? The package has changed a lot since 1.0.1, including in places that appear relevant to your problem. Best wishes Wolfgang On 11/29/11 3:30 PM, Georg Otto wrote: > Dear Bioconductors, > > > I am trying to use DEXSeq to test for differential exon usage in my > RNA-seq data. I was able to generate the exon count tables using the > python scripts that come with the package and the function > read.HTSeqCounts(). However, I get an error at this step: > > 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 > > Any idea what might be wrong here? > > Here is the output of sessionInfo() > > > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DEXSeq_1.0.1 DESeq_1.6.1 locfit_1.5-6 > [4] lattice_0.19-26 akima_0.5-4 Biobase_2.14.0 > [7] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 > > loaded via a namespace (and not attached): > [1] annotate_1.30.0 AnnotationDbi_1.14.1 biomaRt_2.8.1 > [4] Biostrings_2.20.1 BSgenome_1.20.0 DBI_0.2-5 > [7] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 > [10] hwriter_1.3 plyr_1.6 RColorBrewer_1.0-2 > [13] RCurl_1.7-0 RSQLite_0.10.0 rtracklayer_1.12.4 > [16] splines_2.13.0 statmod_1.4.14 stringr_0.5 > [19] survival_2.36-9 tools_2.13.0 XML_3.4-3 > [22] xtable_1.6-0 > > > > Cheers, > > Georg > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
dexseq • 475 views
ADD COMMENTlink modified 8.0 years ago by Georg Otto120 • written 8.0 years ago by Wolfgang Huber13k
Answer: error in DEXSeq fitDispersionFunction()
0
gravatar for Georg Otto
8.0 years ago by
Georg Otto120
Georg Otto120 wrote:
Wolfgang Huber <whuber at="" embl.de=""> writes: Dear Wolfgang, thanks for your help. I tried with version 1.1.1 and still got the same message: 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 Apparently in the function fitDispersionFunction(), the expression sum(log(coefs/oldcoefs)^2) produces NAs with my data, so if (sum(log(coefs/oldcoefs)^2) < 0.005) gives an error... any idea, how to fix this? Cheers, Georg > Dear Georg > > Thank you. Can you please try with a more recent version of DEXSeq, > e.g. 1.1.1 from the last release? The package has changed a lot since > 1.0.1, including in places that appear relevant to your problem. > > Best wishes > Wolfgang > > > > On 11/29/11 3:30 PM, Georg Otto wrote: >> Dear Bioconductors, >> >> >> I am trying to use DEXSeq to test for differential exon usage in my >> RNA-seq data. I was able to generate the exon count tables using the >> python scripts that come with the package and the function >> read.HTSeqCounts(). However, I get an error at this step: >> >> 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 >> >> Any idea what might be wrong here? >> >> Here is the output of sessionInfo() >> >> >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] DEXSeq_1.0.1 DESeq_1.6.1 locfit_1.5-6 >> [4] lattice_0.19-26 akima_0.5-4 Biobase_2.14.0 >> [7] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.30.0 AnnotationDbi_1.14.1 biomaRt_2.8.1 >> [4] Biostrings_2.20.1 BSgenome_1.20.0 DBI_0.2-5 >> [7] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 >> [10] hwriter_1.3 plyr_1.6 RColorBrewer_1.0-2 >> [13] RCurl_1.7-0 RSQLite_0.10.0 rtracklayer_1.12.4 >> [16] splines_2.13.0 statmod_1.4.14 stringr_0.5 >> [19] survival_2.36-9 tools_2.13.0 XML_3.4-3 >> [22] xtable_1.6-0 >> >> >> >> Cheers, >> >> Georg >> >> _______________________________________________ >> 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
ADD COMMENTlink written 8.0 years ago by Georg Otto120
Dear Georg thank you for your feedback. I am afraid you have found a bug. I have contacted you privately (outside this list), ideally we can use your dataset in order to troubleshoot and fix this. Thank you and best wishes Wolfgang On 12/5/11 8:03 PM, Georg Otto wrote: > Wolfgang Huber<whuber at="" embl.de=""> writes: > > Dear Wolfgang, > > thanks for your help. I tried with version 1.1.1 and still got the same > message: > > 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 > > Apparently in the function fitDispersionFunction(), the expression > > sum(log(coefs/oldcoefs)^2) > > produces NAs with my data, so > > if (sum(log(coefs/oldcoefs)^2)< 0.005) > > gives an error... any idea, how to fix this? > > Cheers, > > Georg > > >> Dear Georg >> >> Thank you. Can you please try with a more recent version of DEXSeq, >> e.g. 1.1.1 from the last release? The package has changed a lot since >> 1.0.1, including in places that appear relevant to your problem. >> >> Best wishes >> Wolfgang >> >> >> >> On 11/29/11 3:30 PM, Georg Otto wrote: >>> Dear Bioconductors, >>> >>> >>> I am trying to use DEXSeq to test for differential exon usage in my >>> RNA-seq data. I was able to generate the exon count tables using the >>> python scripts that come with the package and the function >>> read.HTSeqCounts(). However, I get an error at this step: >>> >>> 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 >>> >>> Any idea what might be wrong here? >>> >>> Here is the output of sessionInfo() >>> >>> >>> R version 2.13.0 (2011-04-13) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] DEXSeq_1.0.1 DESeq_1.6.1 locfit_1.5-6 >>> [4] lattice_0.19-26 akima_0.5-4 Biobase_2.14.0 >>> [7] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.30.0 AnnotationDbi_1.14.1 biomaRt_2.8.1 >>> [4] Biostrings_2.20.1 BSgenome_1.20.0 DBI_0.2-5 >>> [7] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 >>> [10] hwriter_1.3 plyr_1.6 RColorBrewer_1.0-2 >>> [13] RCurl_1.7-0 RSQLite_0.10.0 rtracklayer_1.12.4 >>> [16] splines_2.13.0 statmod_1.4.14 stringr_0.5 >>> [19] survival_2.36-9 tools_2.13.0 XML_3.4-3 >>> [22] xtable_1.6-0 >>> >>> >>> >>> Cheers, >>> >>> Georg >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD REPLYlink written 8.0 years ago by Wolfgang Huber13k
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