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renozao / FAQR

Frequently Asked Questions on R: my personal Ask Just Once system for my friends' R problems...
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GEO Annotations #3

Open Rachelly opened 11 years ago

Rachelly commented 11 years ago

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 commented 11 years ago

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

— Reply to this email directly or view it on GitHubhttps://github.com/renozao/FAQR/issues/3 .