[BioC] GO Term Enrichment Analysis for ath1121501

[James W. MacDonald]

Hi Suganya,

On 11/19/2012 6:41 AM, suganya [guest] wrote:
> Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations:
>
> My data is as follows:
> myd #str(myd)
> chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ...
>
> wolunilist# set of selected genes(DEG): str(wolunilist)
> chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ...
>
>
> The coding I used was :
> locus<- unlist(get(myd, ath1121501ACCNUM))
> selected<-unlist(get(wolunilist,ath1121501ACCNUM))

Note that get() assumes you are passing in a single ID. You want mget().

Best,

Jim



> params<- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501",
> +               ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over")
> hgOver<- hyperGTest(params)
>
> And I get the following error:
> debugging in: getUniverseHelper(probes, datPkg, entrezIds)
> debug: {
>      univ<- unique(unlist(mget(probes, ID2EntrezID(datPkg))))
>      if (!missing(entrezIds)&&  !is.null(entrezIds)&&  length(entrezIds)>
>          0)
>          univ<- intersect(univ, unlist(entrezIds))
>      if (length(univ)<  1)
>          stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n  Check input values to confirm they are the same type as the central ID used by your annotation package.\n  For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).")
>      univ
> }
>
> I tried several possibilities but did not succeed.
>
>
>
>
>
>
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: i686-redhat-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
>   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] annaffy_1.28.0       KEGG.db_2.7.1        GO.db_2.7.1          GOstats_2.22.0       graph_1.34.0
>   [6] Category_2.22.0      ath1121501.db_2.7.1  org.At.tair.db_2.7.1 RSQLite_0.10.0       DBI_0.2-5
> [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9  limma_3.12.3         affy_1.34.0          Biobase_2.16.0
> [16] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         annotate_1.34.1       genefilter_1.38.0     GSEABase_1.18.0
>   [5] IRanges_1.14.4        preprocessCore_1.18.0 RBGL_1.32.1           splines_2.15.2
>   [9] stats4_2.15.2         survival_2.36-14      tools_2.15.2          XML_3.9-4
> [13] xtable_1.6-0          zlibbioc_1.2.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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