Hi Iain, I'm not sure what this error is but how does the pwf look when you run nullp()? Does it look like a reasonable distribution? Are you using the Wallenius approximation? Might be worth trying with method="Sampling" and see if you get the same error. Cheers, Alicia On 11/02/12 10:00 PM, "bioconductor-request at r-project.org" <bioconductor-request at="" r-project.org=""> wrote: > Date: Fri, 10 Feb 2012 13:22:17 +0000 > From: Iain Gallagher <iaingallagher at="" btopenworld.com=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] GOSeq error > Message-ID: > <1328880137.28802.YahooMailNeo at web86706.mail.ird.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello List > > I'm using GOSeq to examine the biology behind genes found to be regulated in a > RNA-Seq study. One of my comparisons yields ~450 regulated genes. Attempting > to run GOSeq with this list results in the following error: > > Error in if (min(fv) < lower_bound) fv = fv - min(fv) + lower_bound : > ? missing value where TRUE/FALSE needed > > > The same script works flawlessly (or at least gives me biologically relevant > answers) with other comparisons. > > Could anyone shed any light on this error message? Is it simply indicative of > a lack of significant enrichment? > > > Thanks > > Iain > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_GB.utf8?????? LC_NUMERIC=C???????????? > ?[3] LC_TIME=en_GB.utf8??????? LC_COLLATE=en_GB.utf8??? > ?[5] LC_MONETARY=en_GB.utf8??? LC_MESSAGES=en_GB.utf8?? > ?[7] LC_PAPER=C??????????????? LC_NAME=C??????????????? > ?[9] LC_ADDRESS=C????????????? LC_TELEPHONE=C?????????? > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C????? > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base???? > > other attached packages: > ?[1] reshape2_1.2.1???????? annotate_1.32.1??????? KEGG.db_2.6.1???????? > ?[4] GO.db_2.6.1??????????? goseq_1.6.0??????????? geneLenDataBase_0.99.8 > ?[7] BiasedUrn_1.04???????? org.Bt.eg.db_2.6.4???? RSQLite_0.11.1??????? > [10] DBI_0.2-5????????????? AnnotationDbi_1.16.11? Biobase_2.14.0??????? > [13] edgeR_2.4.3??????????? limma_3.10.2????????? > > loaded via a namespace (and not attached): > ?[1] biomaRt_2.10.0??????? Biostrings_2.22.0???? BSgenome_1.22.0????? > ?[4] GenomicFeatures_1.6.7 GenomicRanges_1.6.6?? grid_2.14.1????????? > ?[7] IRanges_1.12.5??????? lattice_0.20-0??????? Matrix_1.0-3???????? > [10] mgcv_1.7-13?????????? nlme_3.1-103????????? plyr_1.7.1?????????? > [13] RCurl_1.9-5?????????? rtracklayer_1.14.4??? stringr_0.6????????? > [16] tools_2.14.1????????? XML_3.9-2???????????? xtable_1.6-0???????? > [19] zlibbioc_1.0.0?? ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com

Hi Alicia It's the pwf function that falls down. Sorry should have mentioned that before i.e. pwf=nullp(genes,'bosTau4','ensGene') Loading bosTau4 length data... Error in if (min(fv) < lower_bound) fv = fv - min(fv) + lower_bound : ? missing value where TRUE/FALSE needed > head(genes) ENSBTAG00000003825 ENSBTAG00000015185 ENSBTAG00000001068 ENSBTAG00000017500 ???????????????? 0????????????????? 0????????????????? 0????????????????? 0 ENSBTAG00000012288 ENSBTAG00000031901? ???????????????? 0????????????????? 0? > length(which(genes==1)) [1] 336 As I said previously, this works without a problem on other comparisons in the same experiment so it's not a reproducible error (well possibly at some level, but that's beyond my ken at the moment). Thanks & best iain ----- Original Message ----- From: Alicia Oshlack <alicia.oshlack@mcri.edu.au> To: bioconductor at r-project.org Cc: Sent: Saturday, 11 February 2012, 11:56 Subject: Re: [BioC] GOseq error Hi Iain, I'm not sure what this error is but how does the pwf look when you run nullp()? Does it look like a reasonable distribution? Are you using the Wallenius approximation? Might be worth trying with method="Sampling" and see if you get the same error. Cheers, Alicia On 11/02/12 10:00 PM, "bioconductor-request at r-project.org" <bioconductor-request at="" r-project.org=""> wrote: > Date: Fri, 10 Feb 2012 13:22:17 +0000 > From: Iain Gallagher <iaingallagher at="" btopenworld.com=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] GOSeq error > Message-ID: > <1328880137.28802.YahooMailNeo at web86706.mail.ird.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello List > > I'm using GOSeq to examine the biology behind genes found to be regulated in a > RNA-Seq study. One of my comparisons yields ~450 regulated genes. Attempting > to run GOSeq with this list results in the following error: > > Error in if (min(fv) < lower_bound) fv = fv - min(fv) + lower_bound : > ? missing value where TRUE/FALSE needed > > > The same script works flawlessly (or at least gives me biologically relevant > answers) with other comparisons. > > Could anyone shed any light on this error message? Is it simply indicative of > a lack of significant enrichment? > > > Thanks > > Iain > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_GB.utf8?????? LC_NUMERIC=C???????????? > ?[3] LC_TIME=en_GB.utf8??????? LC_COLLATE=en_GB.utf8??? > ?[5] LC_MONETARY=en_GB.utf8??? LC_MESSAGES=en_GB.utf8?? > ?[7] LC_PAPER=C??????????????? LC_NAME=C??????????????? > ?[9] LC_ADDRESS=C????????????? LC_TELEPHONE=C?????????? > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C????? > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base???? > > other attached packages: > ?[1] reshape2_1.2.1???????? annotate_1.32.1??????? KEGG.db_2.6.1???????? > ?[4] GO.db_2.6.1??????????? goseq_1.6.0??????????? geneLenDataBase_0.99.8 > ?[7] BiasedUrn_1.04???????? org.Bt.eg.db_2.6.4???? RSQLite_0.11.1??????? > [10] DBI_0.2-5????????????? AnnotationDbi_1.16.11? Biobase_2.14.0??????? > [13] edgeR_2.4.3??????????? limma_3.10.2????????? > > loaded via a namespace (and not attached): > ?[1] biomaRt_2.10.0??????? Biostrings_2.22.0???? BSgenome_1.22.0????? > ?[4] GenomicFeatures_1.6.7 GenomicRanges_1.6.6?? grid_2.14.1????????? > ?[7] IRanges_1.12.5??????? lattice_0.20-0??????? Matrix_1.0-3???????? > [10] mgcv_1.7-13?????????? nlme_3.1-103????????? plyr_1.7.1?????????? > [13] RCurl_1.9-5?????????? rtracklayer_1.14.4??? stringr_0.6????????? > [16] tools_2.14.1????????? XML_3.9-2???????????? xtable_1.6-0???????? > [19] zlibbioc_1.0.0?? ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _______________________________________________ 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