[BioC] GOstats - internal filtering?

[James W. MacDonald]

Hi Andrew,

On 4/23/2012 10:56 AM, Andrew Jaffe wrote:
> > The only GO terms that are tested are those that arise from mapping 
> your Entrez Gene IDs to GO terms.
> Just to be clear, you mean by mapping the 
> *significant*/selected Entrez Gene IDs (say by a differential 
> expression analysis) to GO terms? Because the universe/possible Entrez 
> Gene IDs on the microarray was identical in both examples below.

Right. When I said *your* Entrez Gene IDs I meant the set of significant 
Entrez Gene IDs from your experiment.

Technically speaking, one could always test GO terms that are not 
represented by any of the significant genes in an experiment, but a use 
case for that doesn't readily come to mind.

Best,

Jim


>
> Thanks,
> Andrew
>
> On Mon, Apr 23, 2012 at 10:42 AM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Andrew,
>
>     On 4/20/2012 10:50 PM, Andrew Jaffe wrote:
>     > Hopefully I can get a quick answer to this question about GOstats.
>     >
>     > I'm trying to calculate enrichment for every GO category using
>     the GOstats
>     > package. I would assume that setting the p-value cutoff = 1 with
>     > conditional=FALSE would give me an enrichment odds ratio/p-value
>     for every
>     > GO category in, say, the BP ontology. However, this does not
>     seem to be the
>     > case, as the number of categories returned seems to be a
>     function of the
>     > geneIds supplied:
>     >
>     >> params = new("GOHyperGParams", geneIds = y$ENTREZID[y$p<  0.001],
>     > + universeGeneIds = y$ENTREZID,
>     > + annotation = "hgu133plus2.db",
>     > + ontology = "BP", pvalueCutoff = 1, conditional = FALSE,
>     > + testDirection="over")
>     >> ht=hyperGTest(params)
>     >> nrow(summary(ht))
>     > [1] 6080
>     >
>     >> params2 = new("GOHyperGParams", geneIds = y$ENTREZID[y$p<  0.01],
>     >          universeGeneIds = y$ENTREZID,
>     > + universeGeneIds = y$ENTREZID,
>     > + annotation = "hgu133plus2.db",
>     > + ontology = "BP", pvalueCutoff = 1, conditional = FALSE,
>     > + testDirection="over")
>     >> ht2=hyperGTest(params2)
>     >> nrow(summary(ht2))
>     > [1] 7856
>     >
>     > Does the HyperGTest function drop GO categories without any
>     genes in them
>     > prior to returning the results table? Or is something else going on?
>
>     Technically, yes. The only GO terms that are tested are those that
>     arise
>     from mapping your Entrez Gene IDs to GO terms.
>
>     Best,
>
>     Jim
>
>
>     >
>     > Thanks,
>     > Andrew
>     >
>     >> sessionInfo()
>     > R version 2.15.0 Patched (2012-04-20 r59123)
>     > Platform: x86_64-unknown-linux-gnu (64-bit)
>     >
>     > locale:
>     >   [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>     >   [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>     >   [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>     >   [7] LC_PAPER=C                     LC_NAME=C
>     >   [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>     > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>     >
>     > attached base packages:
>     > [1] stats     graphics  grDevices datasets  utils     methods   base
>     >
>     > other attached packages:
>     >   [1] GO.db_2.7.1          sva_3.2.0            mgcv_1.7-13
>     >   [4] corpcor_1.6.2        hgu133plus2.db_2.7.1 genefilter_1.38.0
>     >   [7] RColorBrewer_1.0-5   GOstats_2.22.0       Category_2.22.0
>     > [10] org.Hs.eg.db_2.7.1   RSQLite_0.11.1       DBI_0.2-5
>     > [13] funxBox_0.1          digest_0.5.2         multtest_2.12.0
>     > [16] GSEABase_1.18.0      graph_1.34.0         annotate_1.34.0
>     > [19] AnnotationDbi_1.18.0 limma_3.12.0         Biobase_2.16.0
>     > [22] BiocGenerics_0.2.0
>     >
>     > loaded via a namespace (and not attached):
>     >   [1] grid_2.15.0      IRanges_1.14.2   lattice_0.20-6   MASS_7.3-17
>     >   [5] Matrix_1.0-6     nlme_3.1-103     RBGL_1.32.0    
>      splines_2.15.0
>     >   [9] stats4_2.15.0    survival_2.36-12 tools_2.15.0     XML_3.9-4
>     > [13] xtable_1.7-0
>     >
>     >       [[alternative HTML version deleted]]
>     >
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>
>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099