WGCNA analysis with NCBI GEO Series Matrix file?
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@mathavanbioinfo-11955
Last seen 2.1 years ago
India

Hello all,

I am trying to find co expression module of different viruses Using WGCNA package, Can  any one tell me how to use "NCBI GEO SOFT files for co expression analysis.That contain probe list with the expression value of sample, duplicate probes are existing.So kindly  share your valuable ideas and suggestions to SOFT files

Thank you

Best Regards

Mathavan M

WGCNA geo data • 1.3k views
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Have you look at the tutorials of WGCNA? You could load the files as the datTraits

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@peter-langfelder-4469
Last seen 8 months ago
United States

I would try to use the GEOQuery to download the data and split them into expression and sample data tables. You then need to make sure the expression data were normalized in a usable way. Then, as Luis said, follow the WGCNA tutorials.

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