pre-proccessing of TCGA data for WGCNA
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txtbookir • 0
@e5a1445e
Last seen 4 weeks ago
Iran

Hi everyone, i wanted to create an expression matrix for WGCNA input. however, it has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA-COAD data to RPKM/FPKM in GDCquery by DeSeq2 and how to filter expression set of genes by FDR to less than 5000, which is ideal for WGCNA as i have 17000 genes in expression set, but i can not add p-value without losing expression set.

thank you so much

TCGAbiolinks WGCNA • 76 views
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