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@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}}

