GEO Annotations

[Rachelly]

Hi,
I downloaded a geo annotation for a GSE, and it seems there are more probes in the GSE than in the annotation. How is this possible?
Thanks,
Rachelly.

mm_gse <- getGEO("gse7187", destdir="C:\Program Files\R\GSEs")[[1]]
library("moe430a.db")
MM_p2genes <-unlist(as.list(moe430aENTREZID[mappedkeys(moe430aENTREZID)]))
length(featureNames(mm_gse))
[1] 22690
dim(moe430aENTREZID)
[1] 21085 2

[renozao]

This is possibly due to control probes not being in the annotation file or,
in your particular example, to probes that are not mapped to an ENTREZ ID.
Check:

head(setdiff(featureNames(mm_gse), keys(moe430a.db)))
tail(setdiff(featureNames(mm_gse), keys(moe430a.db)))

head(setdiff(featureNames(mm_gse), mappedkeys(moe430aENTREZID)))
tail(setdiff(featureNames(mm_gse), mappedkeys(moe430aENTREZID)))

On 30 October 2013 12:05, Rachelly notifications@github.com wrote:

Hi,
I downloaded a geo annotation for a GSE, and it seems there are more
probes in the GSE than in the annotation. How is this possible?
Thanks,
Rachelly.

mm_gse <- getGEO("gse7187", destdir="C:\Program Files\R\GSEs")[[1]]
library("moe430a.db")
MM_p2genes <-unlist(as.list(moe430aENTREZID[mappedkeys(moe430aENTREZID)]))
length(featureNames(mm_gse))
[1] 22690
dim(moe430aENTREZID)
[1] 21085 2

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