Entering edit mode
7 months ago
Adrij Pawan
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0
I am working on RNA -seq data analysis, I have quantified my data using Salmon which has given me TPM values for all transcripts. Next, I want to perform Weighted gene coexpression analysis (WGCNA) using transcript TPM values. Is there a direct way to do this? or Do I have to preprocess the TPM values before going the WGCNA?
Why TPM? WGCNA is performed with log-transformed gene counts
I understand TPM values can not be directly used for WGCNA.However, i wish to know if we use TPM values with some additional processing steps?
Please see the following past posts regarding your question:
Is there a way where we can convert TPM to raw read count?
TPM to raw counts