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Question: How To Get Significant Genes From Microarray Experiments Data In Geo
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gravatar for fm271
6.4 years ago by
fm271 • 20
fm271 • 20 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
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modified 4.8 years ago by henry-keen • 10 • written 6.4 years ago by fm271 • 20
2
gravatar for Sean Davis
6.4 years ago by
Sean Davis ♦ 25k
National Institutes of Health, Bethesda, MD
Sean Davis ♦ 25k 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 COMMENT • link modified 6.4 years ago • written 6.4 years ago by Sean Davis ♦ 25k

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 REPLY • link modified 6.4 years ago • written 6.4 years ago by fm271 • 20

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 REPLY • link written 6.4 years ago by Sean Davis ♦ 25k
0
gravatar for henry-keen
4.8 years ago by
henry-keen • 10
United States
henry-keen • 10 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 COMMENT • link written 4.8 years ago by henry-keen • 10
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