Question: GOSeq error
gravatar for Iain Gallagher
6.2 years ago by
United Kingdom
Iain Gallagher910 wrote:
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???????? 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??
ADD COMMENTlink written 6.2 years ago by Iain Gallagher910
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