Question: how to create input file for WGCNA
0
gravatar for nitishd.dave
14 months ago by
nitishd.dave20
India
nitishd.dave20 wrote:

I have 25 genes and its pearson coefficient with SOS1 gene and want to create a network correlation with it so, can anyone tell me how to do it on WGCNA and how to create its input file.

network analysis • 732 views
ADD COMMENTlink written 14 months ago by nitishd.dave20

You just have the correlation of these genes to just 1 other gene (SOS1) and you do not even have the original expression values?

ADD REPLYlink modified 14 months ago • written 14 months ago by Kevin Blighe42k

Hi kevin, in addition to pearson coefficient we have its probe id, gene id, and function and want to create a network correlation of 25 genes with this sos1 gene for salt tolerance. is it possible??

ADD REPLYlink written 14 months ago by nitishd.dave20
1

All that you require is any type of data-matrix, generally, with genes as rows and samples as columns. For WGCNA, the data does not have to be normally-distributed but should be QC checked and have outliers removed. Then, all that you need to do is to follow the WGCNA Tutorial, as mentioned by Wouter.

ADD REPLYlink modified 3 months ago • written 14 months ago by Kevin Blighe42k
2
gravatar for WouterDeCoster
14 months ago by
Belgium
WouterDeCoster39k wrote:

Please follow the excellent tutorial of WGCNA.

ADD COMMENTlink written 14 months ago by WouterDeCoster39k
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