Question: how to use singular value detection for identification of modules in wgcna
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gravatar for rajasekargutha
3.6 years ago by
India
rajasekargutha30 wrote:

i am using WGCNA and identified 12modules for 6 traits. to further understand the relation between modules and traits some papers mentioned singular value detection for identification . can any one help me how to perform for my data modules. i have followed WGCNA tutorials but I couldn't understand to proceed further. in this paper https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-16 they used for module selection.

snp rna-seq chip-seq next-gen R • 1.2k views
ADD COMMENTlink modified 3.6 years ago by Jean-Karim Heriche22k • written 3.6 years ago by rajasekargutha30
0
gravatar for Jean-Karim Heriche
3.6 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

Have you looked at the relevant references from the paper you linked to, in particular Alter et al. ?
It is simply a matter of applying SVD to the genes x conditions matrix. Figure 7 of Alter et al. should help you interpret the result.

ADD COMMENTlink written 3.6 years ago by Jean-Karim Heriche22k

could you explain little moare as i am new to this work, and if possible post r code for performing SVD. I have identified 12 modules for 6 traits and i want to see the relation between modules and traits.

ADD REPLYlink written 3.6 years ago by rajasekargutha30

could you explain little moare as i am new to this work, and if possible post r code for performing SVD. I have identified 12 modules for 6 traits and i want to see the relation between modules and traits.

ADD REPLYlink written 3.6 years ago by rajasekargutha30
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