Entering edit mode
Md.Mamunur Rashid
▴
260
@mdmamunur-rashid-3595
Last seen 10.3 years ago
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
regards,
Mamun
---------------------------------------------------
sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[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
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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
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