Question: Is it possible to use geometadb to extract sample age from a set of samples in GEO?
gravatar for Tom
3.4 years ago by
Tom30 wrote:

Just a general question, I don't have code as an example yet.

I have >100 geo data sets (GDSXXX). I want to extract the gene expression data for all of the samples above a certain age. I don't want to do this manually, because there are so many data sets, and also I'll have to do this repeatedly in the future.

I was looking into geometadb, I'm wondering if it's possible to use geometadb to read in a soft/series matrix file, get the age data from somewhere (meta file? series matrix file?) and then use this to extract sample name and age for all samples, which I can subsequently parse further.

As I said, I apologise that I don't have code to back this up yet, I was looking at the geometadb, and I'm not sure I can use this package for this purpose, so I'm just wondering if people think/know if it's possible, or if people have advice as to how they parse sample age from geo data set series matrix or soft files.


R geometadb geo • 937 views
ADD COMMENTlink written 3.4 years ago by Tom30
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