Question

is it possible to use TPM in DESeq2 ?

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Hicham ▴ 10

@2952f756

Last seen 22 months ago

Morocco

My question is quite simple, I want to know is it possible to use TPM data to normalize them with DESeq2? and why?

counts Normalization DESeq2 • 11k views

ADD COMMENT • link updated 2.5 years ago by swbarnes2 ★ 1.4k • written 2.5 years ago by Hicham ▴ 10

score 1 · Answer 1 · 2022-05-10

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Kevin Blighe ★ 4.0k

@kevin

Last seen 15 days ago

Republic of Ireland

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:

Kevin

ADD COMMENT • link 2.5 years ago Kevin Blighe ★ 4.0k

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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"

ADD REPLY • link 2.5 years ago Hicham ▴ 10

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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.

ADD REPLY • link 2.5 years ago swbarnes2 ★ 1.4k

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Ah ha, yes, coming via the tximport route and RSEM is okay.

ADD REPLY • link 2.5 years ago Kevin Blighe ★ 4.0k

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But it sounds like the OP only has the TPM pulled from RSEM, and not the whole output.

ADD REPLY • link 2.5 years ago swbarnes2 ★ 1.4k