[BioC] mogene10stprobeset.db error

Maxim deeepersound at googlemail.com
Sat Jul 3 22:02:13 CEST 2010


Hi,

I try to analyze MoGene-1_0-st gene arrays. I used the aroma package
to do this and came up with an expression matrix, but have no clue,
how to assign real gene names to the respective "IDs" (column "item
numbers" after aroma normalization and summarization).

As a workaround I simply tried to load the mogene10stprobeset.db library and did

u<-mget(row.names(x),mogene10stprobesetSYMBOL)

with x being the expression matrix and rownames(x) are the IDs. But
the majority of IDs are unknown:

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
  value for "10471503" not found

But why? This ID is clearly correct:
10471503		chr2:32530629-32530765	chr2	NC_000068.6	+	32530629	32530765	25	---	ENSMUST00000082819
// ENSEMBL // ncrna:snoRNA chromosome:NCBIM37:2:32530629:32530765:1
gene:ENSMUSG00000064753 // chr2 // 100 // 100 // 25 // 25 // 0 ///
ENSMUST00000083292 // ENSEMBL // ncrna:snoRNA
chromosome:NCBIM37:9:15119289:15119425:1 gene:ENSMUSG00000065226 //
chr2 // 72 // 100 // 18 // 25 // 0	main

What is my problem, obviously I miss something?

Maxim



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