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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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I can't follow the tutorial #14

Closed alberto-mora closed 1 year ago

alberto-mora commented 1 year ago

I am following the tutorial but at this point: pyWGCNA_5xFAD = PyWGCNA.WGCNA(name='5xFAD', species='mouse', geneExpPath=geneExp, save=True) I get this error: ValueError: no types given As I am using the data provided for the tutorial I do not know what might be wrong Thanks in advance

nargesr commented 1 year ago

Hi,

I updated 5xFAD_paper.zip. Please download the updated version and let me know if you still have that problem. thank you so much

alberto-mora commented 1 year ago

It worked. Thank you so much! Now im using my own data but the expression values are in FPKM. Would it make any difference to the analysis?

nargesr commented 1 year ago

When you use TPM, the sum of all TPMs in each sample is the same. This makes it easier to compare the proportion of reads that mapped to a gene in each sample. In contrast, with FPKM, the sum of the normalized reads in each sample may be different, and this makes it harder to compare samples directly.

Overall, I would suggest using TPM if you have that information otherwise you can use FPKM but you might get an artificial class due to you're using FPKM...