Dear friends,

I need to perform GO pathway analysis for mouse exon 1.0 ST array using GOstats package.

Here what I have done:

1.       Read CEL data using oligo package

library("pd.moex.1.0.st.v1")
library(oligo)

affyExonFS <- read.celfiles(list.celfiles())

exonCore <- rma(affyExonFS, target='core')

eset<-exprs(exonCore)



2.       Detect significant genes using limma package.

3.       Find significant pathways using GOstats package.

My code is working now, but I still have two questions:

1.       Oligo package with pd.moex.1.0.st.v1 annotation does not provide entrez id, gene symbol etc. They provide transcriptclusterid. Does anyone know in my case, after code in step one, how can I map from transcriptclusterid to entrez id when using oligo and pd.moex.1.0.st.v1 annotation packages?

2.       I was able to map to entrez id using IPA commercial software. Then in GOstats analysis, I used code



params<-new(...,annotation=" mogene10stprobeset.db",...)

or params<-new(...,annotation="org.Mm.eg.db",...)

hgOver<-hyperGTest(params)



Note here I used org.Mm.eg.db  and mogene10stprobeset.db package instead of my original  pd.moex.1.0.st.v1 ( this does not work for GOstats).

The results of significant pathways are slightly different between org.Mm.eg.db   and mogene10stprobeset.db. Does anyone recommend one of them or both are fine?



Thanks!

Daisy

Biostatistician









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