Question: Is it possible to use geometadb to extract sample age from a set of samples in GEO?
0
gravatar for Tom
22 months ago by
Tom20
Tom20 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.

Thanks.

R geometadb geo • 595 views
ADD COMMENTlink written 22 months ago by Tom20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1075 users visited in the last hour