Question: How do I creat an expressionset if there is no GDS listed on the GEO database?
0
gravatar for pgurkirat
6 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?

microarray limma geoquery • 162 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald51k • written 6 months ago by pgurkirat0

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

ADD REPLYlink written 6 months ago by Kevin Blighe200
Answer: How do I creat an expressionset if there is no GDS listed on the GEO database?
1
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald51k 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 6 months ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 469 users visited in the last hour