[BioC] gene set enrichment

[Gordon K Smyth]

Dear Alpesh,

Please keep questions on the Bioconductor mailing list.

The error message says "there is no package called Biobase", which tells 
you that Biobase is required but you haven't installed it.

Best wishes
Gordon

On Mon, 3 Dec 2012, 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
>
>
>> 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

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