Question: How do I creat an expressionset if there is no GDS listed on the GEO database?
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gravatar for pgurkirat
5 weeks 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?

microarray limma geoquery • 82 views
ADD COMMENTlink modified 5 weeks ago by James W. MacDonald50k • written 5 weeks ago by pgurkirat0

Cross-posted on Biostars: https://www.biostars.org/p/375683/

ADD REPLYlink written 5 weeks ago by Kevin Blighe90
Answer: How do I creat an expressionset if there is no GDS listed on the GEO database?
1
gravatar for James W. MacDonald
5 weeks ago by
United States
James W. MacDonald50k wrote:

Have you read the vignette? You can just as easily get data from the GSE entry, or if you want the raw data you can use getGEOSuppFiles. I have personally never used the pipeline you outline, opting instead for getting the GSE directly.

ADD COMMENTlink written 5 weeks ago by James W. MacDonald50k
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