[BioC] goseq problem

[Naomi Altman]

Got it.  I needed an indicator variable for which genes on in the 
gene list - not the actual gene list.  (Amazing how reading the 
manual carefully can help!)

--Naomi


At 10:10 AM 3/28/2011, Naomi Altman wrote:
>After using edgeR to find differentially expressed genes, I tried to 
>follow the instructions in goseq to correct for length bias.
>
>
>  top$table[1:10,1]
>  [1] "ENSG00000138131" "ENSG00000204616" "ENSG00000204876" 
> "ENSG00000118972" "ENSG00000143546" "ENSG00000163993" 
> "ENSG00000012223" "ENSG00000188257"
>  [9] "ENSG00000140403" "ENSG00000059804"
>geneLengths=getlength(top$table[,1],'hg19','ensGene')
>geneLengths[1:10]
>  [1] 3672.0 2033.5 2675.5 3021.0  454.0  512.0 1813.0  911.5 2877.0 3504.0
>
>(so far, so good)
>
>pwf=nullp(top$table[,1],'hg19','ensGene')
>Loading hg19 length data...
>Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed
>
> > sessionInfo()
>R version 2.12.2 (2011-02-25)
>Platform: i386-pc-mingw32/i386 (32-bit)
>
>locale:
>[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
>States.1252    LC_MONETARY=English_United States.1252
>[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
>attached base packages:
>[1] tools     grid      stats     graphics  grDevices 
>utils     datasets  methods   base
>
>other attached packages:
>  [1] goseq_1.2.0            geneLenDataBase_0.99.5 
> BiasedUrn_1.03         qvalue_1.24.0          sagenhaft_1.20.0 SparseM_0.86
>  [7] edgeR_2.0.5            hexbin_1.24.1          DESeq_1.2.1 
> locfit_1.5-6           lattice_0.19-17        akima_0.5-4
>[13] Biobase_2.10.0
>
>loaded via a namespace (and not attached):
>  [1] annotate_1.28.1      AnnotationDbi_1.12.0 
> Biostrings_2.18.4    BSgenome_1.18.3      DBI_0.2-5 genefilter_1.32.0
>  [7] geneplotter_1.28.0   GenomicRanges_1.2.3  IRanges_1.8.9 
> limma_3.6.9          Matrix_0.999375-46   mgcv_1.7-3
>[13] nlme_3.1-98          RColorBrewer_1.0-2   RCurl_1.5-0.1 
>RSQLite_0.9-4        rtracklayer_1.10.6   splines_2.12.2
>[19] survival_2.36-5      tcltk_2.12.2         XML_3.2-0.2 xtable_1.5-6
> >
>
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