How tximport calculate abundance
1
0
Entering edit mode
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
ADD COMMENT
1
Entering edit mode
@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.

ADD COMMENT
0
Entering edit mode

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

Login before adding your answer.

Traffic: 279 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6