My question is quite simple, I want to know is it possible to use TPM data to normalize them with DESeq2? and why?
No. DESeq2 requires raw count data as input.
If you would like to use TPM, then please take a look at these previous answers, which additionally link to other answers:
I found that data I downloaded is quantified using RSEM is it also not directly useful for DESeq2 ?
the description related to my data "tab-delimited data matrix TPM quantified by RSEM for all samples"
Expected counts from RSEM is fine for DESeq. With tximport, you can put the RSEM input into DESeq, and it will even apply offsets for gene length.
Ah ha, yes, coming via the tximport route and RSEM is okay.
But it sounds like the OP only has the TPM pulled from RSEM, and not the whole output.
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