[BioC] GOseq error

[Iain Gallagher]

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 at 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?? 


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