[BioC] Category: testing for non-random chromosomal distribution of DE genes

Paolo Innocenti paolo.innocenti at ebc.uu.se
Wed May 20 09:55:56 CEST 2009

Hi all,

I wanted to test for chromosomal region enriched for my list of DE genes.
I tried with the ChrMapHyperGParams but it looks like that just Human 
and mice are supported (see below).

I am really interested in this approach, and would like to know if it 
would be difficult to implement such support or there is any other 
package out there doing a similar job.

If there is not a 'off the shelf' solution to this, the simplest 
possible question would be if my D.E. genes are enriched in sexual 
chromosomes vs. autosomes. Is there a better approach than a chisq.test?


 > temp.params <- new("ChrMapHyperGParams",
+                  conditional=FALSE,
+                  testDirection="over",
+                  universeGeneIds=univ,
+                  geneIds=id.int,
+                  annotation=annotation(eset),
+                  pvalueCutoff=0.05)
 > temp <- hyperGTest(temp.params)
Error: 'ORGANISM:Drosophila melanogaster' is not a supported.
  organism must be one of: ORGANISM:Homo sapiens, ORGANISM:Mus musculus
 > sessionInfo()
R version 2.9.0 (2009-04-17)


attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
  [1] GOstats_2.10.0        graph_1.22.2          Category_2.10.0
  [4] drosophila2.db_2.2.11 annaffy_1.16.0        affycoretools_1.16.0
  [7] KEGG.db_2.2.11        GO.db_2.2.11          AnnotationDbi_1.6.0
[10] affy_1.22.0           Biobase_2.4.1         RSQLite_0.7-1
[13] DBI_0.2-4

loaded via a namespace (and not attached):
  [1] affyio_1.12.0        annotate_1.22.0      biomaRt_2.0.0
  [4] gcrma_2.16.0         genefilter_1.24.0    grid_2.9.0
  [7] GSEABase_1.6.0       lattice_0.17-22      limma_2.18.0
[10] lme4_0.999375-28     Matrix_0.999375-26   MCMCglmm_1.09
[13] preprocessCore_1.6.0 RBGL_1.20.0          RCurl_0.94-1
[16] splines_2.9.0        survival_2.35-4      tools_2.9.0
[19] XML_2.3-0            xtable_1.5-5

Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden

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