Finding Entrez geneIDs from a GEO expression set object in R
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8 weeks ago
petrandent ▴ 20

Hello, I was wondering if it is possible from a GEO object to transform the probe IDs to Entrez IDs. The only thing I have found after day of looking for an answer around , is something like that

geo1=getGEO("GSE56532") ;

geo_glob<-geo1[[1]];

geo_glob@featureData@data$gene_assignment

But the result looks chaotic, and doesn't let me map the IDs on the GEO object to Entrez IDs.

I have tried biomaRt... however I cannot find a way to extract from a GEO object the microarray platform in order to set this as an argument on the getBM function.

I am wondering if there is an answer of how to extract these specific information from a GEO object like the one above.

GEO R • 106 views
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