Question

How tximport calculate abundance

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chendianyu • 0

@chendianyu-21982

Last seen 4.2 years ago

Hi, I'm using tximport to combine RSEM .genes.results output for downstream DEG analysis, and I get abundance and counts in the tximport object. So I'm wondering how tximport calculate abundance, is it similar to FPKM?
Any suggestions? Thanks.

tximport abundance • 953 views

ADD COMMENT • link updated 4.4 years ago by Michael Love 43k • written 4.4 years ago by chendianyu • 0

score 1 · Accepted Answer · 2020-08-03

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Michael Love 43k

@mikelove

Last seen 6 days ago

United States

Abundance for the gene is the sum of the abundance values of the isoforms if you use tximport to summarize (that is, if you import isoform level results). This is the same as RSEM does in the genes results files.

ADD COMMENT • link 4.4 years ago Michael Love 43k

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Thanks for your reply! Yes, I checked the original RSEM *.genes.results file and tximport object, finding that counts is corresponding to the expected_count column in *.genes.results file and abundance is corresponding to the TPM column in *.genes.results file

ADD REPLY • link 4.4 years ago chendianyu • 0