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Data transformation options for analysing TCGA transcriptome data #3

Open jijitoutou opened 5 months ago

jijitoutou commented 5 months ago

Dear Professor,

I am currently planning to analyze transcriptome data from The Cancer Genome Atlas (TCGA) project using this R package for my analysis. Given the various data transformation options available, such as Counts Per Million (CPM), voom-transformed counts, and log2-transformed Transcripts Per Million (TPM) + 1. I seek your guidance on which data format would be most suitable for analysis with this R package.

Thank you very much for your time and assistance.

WangX-Lab commented 5 months ago

log2(TPM+1) should be better.

---- Replied Message ---- From jijitoutou @.> Date 03/27/2024 21:23 To WangX-Lab/DEPTH @.> Cc Subscribed @.***> Subject [WangX-Lab/DEPTH] Data transformation options for analysing TCGA transcriptome data (Issue #3)

Dear Professor, I am currently planning to analyze transcriptome data from The Cancer Genome Atlas (TCGA) project using this R package for my analysis. Given the various data transformation options available, such as Counts Per Million (CPM), voom-transformed counts, and log2-transformed Transcripts Per Million (TPM) + 1. I seek your guidance on which data format would be most suitable for analysis with this R package. Thank you very much for your time and assistance. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

jijitoutou commented 5 months ago

log2(TPM+1) should be better. … ---- Replied Message ---- From jijitoutou @.> Date 03/27/2024 21:23 To WangX-Lab/DEPTH @.> Cc Subscribed @.> Subject [WangX-Lab/DEPTH] Data transformation options for analysing TCGA transcriptome data (Issue #3) Dear Professor, I am currently planning to analyze transcriptome data from The Cancer Genome Atlas (TCGA) project using this R package for my analysis. Given the various data transformation options available, such as Counts Per Million (CPM), voom-transformed counts, and log2-transformed Transcripts Per Million (TPM) + 1. I seek your guidance on which data format would be most suitable for analysis with this R package. Thank you very much for your time and assistance. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you for your advice.