[BioC] SeqGSEA estiGeneNBstat()

[Kasoji, Manjula (NIH/NCI) [C]]

Hi Xi,

Thank you for your suggestion. I have pasted the information that you requested below. It seems testable is TRUE however Nbstat is FALSE for the the entire table.

What should I do in this situation?


> head(counts at featureData@data)
                     exonIDs              geneIDs testable prob_case prob_ctrl var_case var_ctrl NBstat pvalue padjust
alignment_not_unique     ENA alignment_not_unique     TRUE        NA        NA       NA       NA     NA     NA      NA
ambiguous                ENA            ambiguous     TRUE        NA        NA       NA       NA     NA     NA      NA
ENSMUSG00000000001       ENA   ENSMUSG00000000001     TRUE        NA        NA       NA       NA     NA     NA      NA
ENSMUSG00000000028       ENA   ENSMUSG00000000028     TRUE        NA        NA       NA       NA     NA     NA      NA
ENSMUSG00000000037       ENA   ENSMUSG00000000037     TRUE        NA        NA       NA       NA     NA     NA      NA
ENSMUSG00000000049       ENA   ENSMUSG00000000049     TRUE        NA        NA       NA       NA     NA     NA      NA


I appreciate your help!
From: Xi Wang <xi.wang at newcastle.edu.au<mailto:xi.wang at newcastle.edu.au>>
Date: Tuesday, June 25, 2013 8:38PM
To: "SeqGSEA-user [guest]" <guest at bioconductor.org<mailto:guest at bioconductor.org>>
Cc: "bioconductor at r-project.org<mailto:bioconductor at r-project.org>" <bioconductor at r-project.org<mailto:bioconductor at r-project.org>>, "Kasoji, Manjula (NIH/NCI) [C]" <manjula.kasoji at nih.gov<mailto:manjula.kasoji at nih.gov>>
Subject: Re: SeqGSEA estiGeneNBstat()

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 at 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 at bioconductor.org<mailto:guest at 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
>

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