Go Term Enrichment Analysis For Ath1121501

Question

[suganyasivagurunathan]

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)) # in this case it only fetches a single id
 head(locus) [1] "ATMG00640"
selected<-unlist(get(wolunilist,ath1121501ACCNUM))# in this case it only fetches a single id
head(selected) [1] "ATMG00640"
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 :

mget(c("244901_at", "244902_at", "244903_at", "244904_at", "244905_at"),ath1121501ACCNUM)

I get:

$`244901_at`
[1] "ATMG00640"

$`244902_at`
[1] "ATMG00650"

$`244903_at`
[1] "ATMG00660"

$`244904_at`
[1] "ATMG00670"

$`244905_at`
[1] "ATMG00680"

sel<-unlist(mget(wolunilist,ath1121501ACCNUM))
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
  value for "245651_s_at" not found

I am unable to figure out where am going wrong.If I do for a few ids , Iam able to do but if I store it as a character vector I get the above error.

 -- 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

[Pierre Lindenbaum]

cross posted on SO: http://stackoverflow.com/questions/13453129

Answer 1

[Nick Crawford]

Have you considered using a standalone GO analysis package like GO elite?

http://www.genmapp.org/go_elite/

Answer 2

[zhangmin8712]

  you should use "mget" function to get the accession IDs of probes. Like, 
  > list
  [1] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at"
  > unlist(mget(list,ath1121501ACCNUM))      ### mget
    244901_at   244902_at   244903_at   244904_at   244905_at   244906_at 
  "ATMG00640" "ATMG00650" "ATMG00660" "ATMG00670" "ATMG00680" "ATMG00690" 
  > unlist(get(list,ath1121501ACCNUM))    ### get
  [1] "ATMG00640"