How tximport calculate abundance
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chendianyu • 0
@chendianyu-21982
Last seen 13 months 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 • 191 views
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@mikelove
Last seen 7 hours 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.

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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