Question: (Closed) How do I creat an expressionset if there is no GDS listed on the GEO database?
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gravatar for pgurkirat
11 months ago by
pgurkirat0
pgurkirat0 wrote:

Hello

I have been using the GEOquery package to create expression sets from data taken from NCBI gene expression omnibus (GEO) database. However, I have ran into a problem. Most of the studies that are useful to me do not have a GDS listed. They have GSE, GSM, and GPL but, I use the command gds<-getGEO("GDS4061") to start with, and then do eset <- GDS2eSet(gds,do.log2=TRUE) to convert GDS into an expression set, so I assume the GDS class is necessary. Can somebody suggest how to overcome this problem please?

Thank you

ADD COMMENTlink written 11 months ago by pgurkirat0

Cross-posted on Bioconductor: https://support.bioconductor.org/p/120226/

ADD REPLYlink written 11 months ago by Kevin Blighe56k

Hello pgurkirat!

We believe that this post does not fit the main topic of this site.

Cross-posted and answered on Bioconductor

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 11 months ago by Kevin Blighe56k
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