Question: How To Get Significant Genes From Microarray Experiments Data In Geo
0
gravatar for fm271
6.4 years ago by
fm27120
fm27120 wrote:

Is there a way to download microarray experiments in GEO, which have gene names and the corresponding p-value and fold change (optional). I need to find significant genes in those random experiments.

geo microarray download • 2.1k views
ADD COMMENTlink modified 4.8 years ago by henry-keen10 • written 6.4 years ago by fm27120
2
gravatar for Sean Davis
6.4 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

It is not possible to get this information in any general way from NCBI GEO. You could use the online GEO2R system or you could use GEOquery and limma, for example, to access and then perform analyses of your choice from R and Bioconductor.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Sean Davis25k

I was trying exactly the same thing. I am exploring GEO2R. I think I can do that now using the generated R-script.

Is there an automatic way to detect the groups within the sample?

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by fm27120

No, there is not an automated way to detect groups within the sample. This is simply a function of the GEO data model which does not describe groups in a computable way.

ADD REPLYlink written 6.4 years ago by Sean Davis25k
0
gravatar for henry-keen
4.8 years ago by
henry-keen10
United States
henry-keen10 wrote:

Use GEO datasets (not series).  Look in the soft files corresponding to GEO datasets. Here, the samples are described and grouped into subsets.

ADD COMMENTlink written 4.8 years ago by henry-keen10
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