Question: Clinical data from GEO
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gravatar for landscape95
3.0 years ago by
landscape95170
landscape95170 wrote:

Dear everyone,

I am doing analysis from GEO database, I download the soft files, extract the expression matrix of probes-to-sample but I don't know where to find clinical data for these sample for further survival analysis. Could you please guide me how to do this.

For example this GSE data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse10780

Thank you!

geo • 2.3k views
ADD COMMENTlink modified 3.0 years ago by Istvan Albert ♦♦ 84k • written 3.0 years ago by landscape95170
2
gravatar for Istvan Albert
3.0 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

Reproducibility is huge problem and most distribution systems like GEO are not well suited for distributing data other than a few simple and known types like fastq, fasta etc.

Here is what you can do:

  1. Check the supplementary data in the paper - these typically are notoriously obtuse and convoluted to deal with. Often are not described in sufficient detail hence you will need to download and open each to see what is inside them.
  2. Your actual best bet is to contact the authors and ask for this data (or have them point out where this data is).
ADD COMMENTlink written 3.0 years ago by Istvan Albert ♦♦ 84k

Thank you very much, Professor Istvan Albert

ADD REPLYlink written 3.0 years ago by landscape95170
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