How To Get Significant Genes From Microarray Experiments Data In Geo
2
0
Entering edit mode
11.1 years ago
fm271 ▴ 20

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.

microarray geo • 3.3k views
ADD COMMENT
2
Entering edit mode
11.1 years ago

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode
9.5 years ago
henry-keen ▴ 40

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

Login before adding your answer.

Traffic: 1421 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6