Entering edit mode
John Coulthard
▴
170
@john-coulthard-3077
Last seen 10.2 years ago
Hi
Could someone please help me out with this error on a hyperGTest with
KEGG parameters? I get the same error on the hgu133plus2 chip. Must be
something wrong with my parameter definition but I can't work out
what.
> params<-new("KEGGHyperGParams", geneIds =entrez_set0.05,
universeGeneIds = character(0), annotation = "mouse4302",
testDirection
="over")
> hgkegg<- hyperGTest(params)
Error in get(paste(lib, name, sep = "")) :
variable "mouse4302PATH2EG" was not found
More details below.
Many thanks
John
> class(entrez_set0.05)
[1] "character"
> head(entrez_set0.05)
[1] "2673" "3977" "687" "54510" "51101" "6926"
> ls("package:mouse4302.db")
[1] "mouse4302" "mouse4302ACCNUM"
"mouse4302ALIAS2PROBE"
[4] "mouse4302CHR" "mouse4302CHRLENGTHS"
"mouse4302CHRLOC"
[7] "mouse4302CHRLOCEND" "mouse4302_dbconn"
"mouse4302_dbfile"
[10] "mouse4302_dbInfo" "mouse4302_dbschema"
"mouse4302ENSEMBL"
[13] "mouse4302ENSEMBL2PROBE" "mouse4302ENTREZID"
"mouse4302ENZYME"
[16] "mouse4302ENZYME2PROBE" "mouse4302GENENAME" "mouse4302GO"
[19] "mouse4302GO2ALLPROBES" "mouse4302GO2PROBE" "mouse4302MAP"
[22] "mouse4302MAPCOUNTS" "mouse4302MGI"
"mouse4302MGI2PROBE"
[25] "mouse4302ORGANISM" "mouse4302PATH"
"mouse4302PATH2PROBE"
[28] "mouse4302PFAM" "mouse4302PMID"
"mouse4302PMID2PROBE"
[31] "mouse4302PROSITE" "mouse4302REFSEQ"
"mouse4302SYMBOL"
[34] "mouse4302UNIGENE" "mouse4302UNIPROT"
> params<-new("KEGGHyperGParams", geneIds =entrez_set0.05,
universeGeneIds = character(0), annotation = "mouse4302",
testDirection ="over")
> hgkegg<- hyperGTest(params)
Error in get(paste(lib, name, sep = "")) :
variable "mouse4302PATH2EG" was not found
>
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-redhat-linux-gnu
locale:
LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.u
tf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C
;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATI
ON=C
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] gtools_2.5.0 GOstats_2.8.0 Category_2.8.3
[4] genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0
[7] annotate_1.20.1 xtable_1.5-5 GO.db_2.2.5
[10] graph_1.20.0 RMySQL_0.7-2 KEGG.db_2.2.5
[13] mouse4302.db_2.2.5 moe430b.db_2.2.5 RSQLite_0.7-1
[16] DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.2
loaded via a namespace (and not attached):
[1] cluster_1.11.11 GSEABase_1.4.0 XML_1.98-1
_________________________________________________________________
[[elided Hotmail spam]]
[[alternative HTML version deleted]]