What's the real mean of expression data/level

drostlab / myTAI

Evolutionary Transcriptomics with R

https://drostlab.github.io/myTAI/

GNU General Public License v2.0

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What's the real mean of expression data/level #10

Closed Chenleinice closed 1 year ago

Chenleinice commented 2 years ago

Dear Dr. Hajk-Georg Drost Great work on the integration of gene evolution and transcriptome. However, I‘m confused about what's expression data, TPM, FPKM, or just read counts? Many thanks for your help! Yours sincerely, Lei Chen

HajkD commented 2 years ago

Dear Lei Chen,

Thank you for your question and glad to hear you find myTAI useful.

Expression data assumes TPMs normalized across developmental stages so that 'absolute TPM' values can be compared between developmental stages (/replicates).

I hope this helps!

Cheers, Hajk

HajkD commented 1 year ago

P.s. If helper packages such as edgeR or DESeq2 are used for differential gene expression analysis, then ExpressionSet refers to the count or normalised count matrices expected by edgeR or DESeq2.