Question: WGCNA data format?
0
gravatar for michael.ridley6
3.7 years ago by
United Kingdom
michael.ridley60 wrote:

Currently grappling with the WGCNA package for the first time and worked through the tutorials provided, and now trying to look at my own data with this technique.

However, im unsure what format my data needs to be in (log2/linear/etc)?,

Ive checked the website again and again, and cannot find the answer.

microarray wgcna coexpression • 1.8k views
ADD COMMENTlink modified 3.7 years ago by Peter Langfelder2.1k • written 3.7 years ago by michael.ridley60
Answer: WGCNA data format?
0
gravatar for Peter Langfelder
3.7 years ago by
United States
Peter Langfelder2.1k wrote:

I usually recommend log-transformed data, although this may depend on pre-processing and normalization. The idea is to use data for which random errors are approximately symmetric and, if possible, not too heavy-tailed. Note that some microarray normalization methods, notably RMA for Affy arrays and some schemes for Agilent arrays, return log-transformed data. For RNA-seq, see the WGCNA FAQ at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html, especially point 3.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Peter Langfelder2.1k
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