How To Get Significant Genes From Microarray Experiments Data In Geo

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

• 4,081 views • link

updated 3.4 years ago by Ram

• written 13.4 years ago by fm271 •

2 answers

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.

• 17 views • link

updated 5.4 years ago by Ram

• written 13.4 years ago by Sean Davis

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?

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updated 5.4 years ago by Ram

• written 13.4 years ago by fm271 •

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.

• 0 views • link

updated 5.4 years ago by Ram

• written 13.4 years ago by Sean Davis

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

• 0 views • link

updated 5.4 years ago by Ram

• written 11.8 years ago by henry-keen •

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