Entering edit mode
Dai, Hongying,
▴
60
@dai-hongying-4801
Last seen 10.3 years ago
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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