[BioC] obtaining GOID from nuID

Md.Mamunur Rashid mamunur.rashid at kcl.ac.uk
Fri Jan 15 13:48:11 CET 2010

Dear List,

I have some problem with goTools analysis and I hope yet again the great
experts will help me.

I have a list of significant genes and I am trying to use them for GO analysis
using go bioc goTools package.

sigGenes<- Illumina nuID( lumi package) obtained by adjusted p.value filtering.

goIds<- getGO(sigGenes,"lumiHumanAll.db")

probeType<- "GO"
ontology<- "BP"

ontoCompare(list(goIds),probeType = probeType, ontology = ontology, plot = TRUE)

Starting ontoCompare...
Error in goidvect[test] : invalid subscript type 'list'

What I understand , the reason behind this is,  getGO() method returns
more than one GO Ids and terms for each nuID instead of returning a single
GO ID for each nuID.

Is there any way I can resolve this.....???

Thanks in advance

R version 2.10.1 (2009-12-14)

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
  [1] goProfiles_1.8.0               Biobase_2.6.1
  [3] session_1.0.2                  gtools_2.6.1
  [5] limma_3.2.1                    car_1.2-16
  [7] hopach_2.6.0                   cluster_1.12.1
  [9] xtable_1.5-6                   illuminaHumanv3BeadID.db_1.4.1
[11] Cairo_1.4-5                    goTools_1.20.0
[13] GO.db_2.3.5                    GOstats_2.12.0
[15] graph_1.24.1                   Category_2.12.0
[17] lumiHumanIDMapping_1.4.0       lumiHumanAll.db_1.8.1
[19] org.Hs.eg.db_2.3.6             RSQLite_0.8-0
[21] DBI_0.2-5                      preprocessCore_1.8.0
[23] annotate_1.24.0                AnnotationDbi_1.8.1

loaded via a namespace (and not attached):
  [1] affy_1.24.2        affyio_1.14.0      genefilter_1.28.2  grid_2.10.1
  [5] GSEABase_1.8.0     lattice_0.17-26    lumi_1.12.2        MASS_7.3-4
  [9] Matrix_0.999375-33 mgcv_1.6-1         nlme_3.1-96        RBGL_1.22.0
[13] splines_2.10.1     survival_2.35-7    tools_2.10.1       XML_2.6-0

More information about the Bioconductor mailing list