[BioC] GO Term Enrichment Analysis for ath1121501

[James W. MacDonald]

Hi Suganya,

On 11/20/2012 2:59 AM, suganya [guest] wrote:
> 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))
> If I use mget then I get the following error:
>
> Error in checkKeys(value, Lkeys(x), x at ifnotfound) :
>    value for "245651_s_at" not found

This is the point at which I gently remind you that there are help pages 
for all R functions, and they are often helpful. Looking at the help 
page a good idea because a.) asking on a list and waiting for help is 
highly inefficient, and b.) at some point you have to learn to figure 
things out for yourself.

So, typing ?mget at the R prompt, and choosing the 'Environment-like API 
for Bimap objects {AnnotationDbi}' from the list that pops up, I find 
the following on the resulting page:

First,

  mget(x, envir, mode, ifnotfound, inherits)

which shows the API for mget(). If I then look further, I find

ifnotfound: A value to be used if the key is not found. Only NA is
           currently supported.

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():
>
>>    -- 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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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