Extracting Microarray Data From Gse 'Object' Using Geoquery

Question

[cjmcdermottroe]

Hi.

I'm trying to use GEOquery to extract data from a GSE file I downloaded but I'm not having any joy.

Can someone tell me what commands to use?

thanks and sorry if this is covered else where.

Chros

[Neilfws]

It's covered in the GEOquery manual. And it helps if you describe, precisely, what you are trying to do.

Answer 1

[Sean Davis]

I'm guessing this isn't a GEOquery question, really. Assuming you are doing something like:

library(GEOquery)
gseList = getGEO('GSE2553')
gse = gseList[[1]]

Now, gse is an ExpressionSet. See the help for ExpressionSet-class (in the Biobase package) to learn how to use these objects. If this doesn't answer your question, please provide more detail in your question.