Hi I'm having trouble running the estiGeneNBstat() function. Here is the error message I receive: Error in estiGeneNBstat(counts) : Please run estiExonNBstat first. But I have already run the estiExonNBstat() first. I basically just plugged in my data as show in the example in the vignette. Below is my code. I just feed in the counts from estiExonNBstat() into estiGeneNBstat(), so I'm not sure why I'm getting that error. Any insight will be appreciated. Thank you! CODE: #######################################################Step 1: DS analysis # load exon read count data #RCS <- loadExonCountData(case.files, control.files) counts <- loadExonCountData(ps.files, cb.files) # remove genes with low exprssion #RCS <- exonTestability(RCS, cutoff=5) counts <- exonTestability(counts, cutoff=5) geneTestable <- geneTestability(counts) counts <- subsetByGenes(counts, unique(geneID(counts))[ geneTestable ]) # get gene IDs, which will be used in initialization of gene set #geneIDs <- unique(geneID(RCS)) geneIDs <- unique(geneID(counts)) # calculate DS NB statistics counts <- estiExonNBstat(counts) counts <- estiGeneNBstat(counts) -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] SeqGSEA_1.0.2 foreach_1.4.1 biomaRt_2.16.0 DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 [8] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.6 codetools_0.2-8 compiler_3.0.0 DBI_0.2-7 doParallel_1.0.3 [7] genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.0 IRanges_1.18.1 iterators_1.0.6 RColorBrewer_1.0-5 [13] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.0 stats4_3.0.0 survival_2.37-4 tools_3.0.0 [19] XML_3.95-0.2 xtable_1.7-1 > -- Sent via the guest posting facility at bioconductor.org.

Dear user, Thanks for your email. This is the first time encountering this kind of problem. I am wondering if your data were too shallow. Could you please show me more information to help diagnose? Simply type head(counts@featureData@data) after you run counts <- estiExonNBstat(counts) and check the columns with names 'testable' and 'NBstat'. If 'testable' is TRUE and 'NBstat' is not NA, the next step will work. Cheers Xi On Wed, Jun 26, 2013 at 3:55 AM, SeqGSEA-user [guest] < guest@bioconductor.org> wrote: > > Hi I'm having trouble running the estiGeneNBstat() function. > > Here is the error message I receive: > > Error in estiGeneNBstat(counts) : Please run estiExonNBstat first. > > But I have already run the estiExonNBstat() first. I basically just > plugged in my data as show in the example in the vignette. Below is my > code. I just feed in the counts from estiExonNBstat() into > estiGeneNBstat(), so I'm not sure why I'm getting that error. Any insight > will be appreciated. Thank you! > > CODE: > > #######################################################Step 1: DS analysis > # load exon read count data > #RCS <- loadExonCountData(case.files, control.files) > counts <- loadExonCountData(ps.files, cb.files) > > # remove genes with low exprssion > #RCS <- exonTestability(RCS, cutoff=5) > counts <- exonTestability(counts, cutoff=5) > > geneTestable <- geneTestability(counts) > > counts <- subsetByGenes(counts, unique(geneID(counts))[ geneTestable ]) > > # get gene IDs, which will be used in initialization of gene set > #geneIDs <- unique(geneID(RCS)) > geneIDs <- unique(geneID(counts)) > > # calculate DS NB statistics > counts <- estiExonNBstat(counts) > counts <- estiGeneNBstat(counts) > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] SeqGSEA_1.0.2 foreach_1.4.1 biomaRt_2.16.0 DESeq_1.12.0 > lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 > [8] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationDbi_1.22.6 codetools_0.2-8 > compiler_3.0.0 DBI_0.2-7 doParallel_1.0.3 > [7] genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.0 > IRanges_1.18.1 iterators_1.0.6 RColorBrewer_1.0-5 > [13] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.0 > stats4_3.0.0 survival_2.37-4 tools_3.0.0 > [19] XML_3.95-0.2 xtable_1.7-1 > > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]