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3 days ago
TNF_alpha
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Use ssGSEA: Input: Log-transformed TPM of TCGA tumor samples only & a list of angiogenesis related genes. Output: angiogenesis scores (one per tumor sample).
Perform WGCNA: Input: Raw counts for the same tumor samples. Normalize with DESeq2 (VST). Build the network and identify modules.
Correlate angiogenesis Scores With Modules: Relate module eigengenes to ssGSEA scores to identify angiogenesis-related gene modules.
1) IS THIS WORKFLOW CORRECT? 2) Can I take only Tumor samples for both ssGSEA and WGCNA? or I have to take Normal samples as well. 3) As my angiogenesis gene list is manually collected, some genes are highly expressed in tumor samples and some in normal samples....will it affect the ssGSEA score?
