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petitmingchang / TO-GCN

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data
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Can TPM be used as input data? #14

Closed Nuturetree closed 9 months ago

Nuturetree commented 12 months ago

Hello, I wanted to reach out and express my appreciation for your work on To-GCN, a valuable tool for analyzing 3D transcriptomes. I have thoroughly reviewed the methodology outlined in your article, and based on the information provided, I would like to confirm whether TPM (Transcripts Per Million) values can be used as valid input data. I look forward to your response. Best regards, Nutures.

jordan841220 commented 9 months ago

Follow up with this question...in the paper the RPKM values were further underwent upper-quartile normalization before the construction of GCNs. Is this normalization necessary? @petitmingchang

petitmingchang commented 9 months ago

@Nuturetree and @JordanCTLin Yes, Both "between sample normalized" TPM or FPKM values can be used as input data.