5 months ago by
Republic of Ireland
You indicate that your data is currently stored in an Excel sheet, which is not typical. From where did you obtain it? Processed RNA-seq data is usually stored in a CSV or TSV file, and may be tarred and zipped and have the extension *.tar.gz. Note that storing and re-using data from an Excel sheet is not good practice. Excel adds a lot of formatting on top of your data and can even modify / manipulate it in ways that you may not anticipate.
I suggest that you go through the entire WGCNA Tutorial and then apply the methodology to your own data.
With tumour-normal data, you may consider one of the following:
- run WGCNA separately for each of tumour and normal and then compare
- run WGCNA with tumour + normal together and then see which modules (and, from this, which genes contained within those modules)
correlate with tumour-normal status.
If you honestly complete the online tutorial even once, you will have a better understanding. That's why the tutorial exists.