[BioC] gene set enrichment

[Martin Morgan]

On 12/03/2012 09:05 AM, Alpesh Querer wrote:
> Thanks Gordon.
>
> I was trying to install the latest version  of R and goseq, but it wouldn't
> load anymore.
> do you have an insight on why this would happen? maybe i`m doing something
> not right.
>
>
>>      biocLite("goseq")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'goseq'
> trying URL '
> http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/goseq_1.10.0.zip
> '
> Content type 'application/zip' length 751702 bytes (734 Kb)
> opened URL
> downloaded 734 Kb
>
> package ‘goseq’ successfully unpacked and MD5 sums checked
>
>
>> library(goseq)
> Loading required package: BiasedUrn
> Loading required package: geneLenDataBase
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>    there is no package called ‘Biobase’
> Error: package ‘geneLenDataBase’ could not be loaded

geneLenDataBase (?) seems to be missing a dependency. Try

   biocLite("Biobase")

first.

Martin

>
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-w64-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiasedUrn_1.04      BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] BiocGenerics_0.4.0   Biostrings_2.26.2    bitops_1.0-5
> BSgenome_1.26.1      DBI_0.2-5            GenomicRanges_1.10.5
> IRanges_1.16.4
>   [8] parallel_2.15.2      RCurl_1.95-3         Rsamtools_1.10.2
> RSQLite_0.11.2       rtracklayer_1.18.1   stats4_2.15.2
> tools_2.15.2
> [15] XML_3.95-0.1         zlibbioc_1.4.0
>
>
> Thanks,
> Al
>
>
>
>
> On Sat, Dec 1, 2012 at 7:39 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> Dear Al,
>>
>> The obvious answer is the goseq package.  However you have already
>> received assistance with goseq:
>>
>>    https://stat.ethz.ch/**pipermail/bioconductor/2012-**
>> February/043779.html<https://stat.ethz.ch/pipermail/bioconductor/2012-February/043779.html>
>>
>> So if you are not trying to do a Gene Ontology analysis like goseq does,
>> what is it that you are trying to do?
>>
>> The term "gene set enrichment analysis" was coined by the Broad Institute:
>>
>>    http://www.broadinstitute.org/**gsea/<http://www.broadinstitute.org/gsea/>
>>
>> but you certainly can't simply give a list of genes to GSEA.  It requires
>> complete data and is designed for microarrays rather than RNA-Seq anyway.
>>
>> Best wishes
>> Gordon
>>
>> ----------------- original message -----------------
>> [BioC] gene set enrichment
>> Alpesh Querer alpeshq at gmail.com
>> Sun Dec 2 01:27:41 CET 2012
>>
>> Hello all,
>>
>> I have list of differentially expressed genes from an rna-seq analysis.
>> Also, I have a two-column annotation file for the organism with the columns
>> being gene and goterm. please guide me towards a bioconductor package or
>> any other tool that I could use my list and annotation file as input and do
>> gene set enrichment analysis.
>>
>> Thanks,
>> Al
>>
>> ______________________________**______________________________**__________
>> The information in this email is confidential and inte...{{dropped:10}}
>
>
>
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