Why the results of quant mode are not integer?

hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

GNU General Public License v3.0

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Why the results of quant mode are not integer? #72

Closed gxAlan233 closed 1 year ago

gxAlan233 commented 1 year ago

I used the quant mode (exprtype is count) but I found that the results are not integer so it could not be used in some packages in R. If the exprtype is raw count, it should come out as integer, right?

Some of my results are as following:

TE	sample1	sample2	sample3
ALU	1161.53	1069.54	1230.75
AluJb	1652.24	1277.59	1612.31
AluJo	305.976	211.666	111.345
AluJr	167.593	258.337	120.824
AluJr4	317.785	345.129	444.774
AluSc	5873.77	5024.22	6805.05
AluSc5	1200.61	2001.05	2773.98

rargelaguet commented 1 year ago

I have the same question :)

hyunhwan-jeong commented 1 year ago

Sorry for the late response. This is related to #23 and #62. My answer is that SalmonTE uses salmon as a core algorithm for the quantification, and quantification is indeed an estimation of both raw counts/TPM. Thus, you can expect to see any floating numbers, and I'd recommend rounding the numbers for your downstream analysis.

Hope it helps,

Hyun-Hwan Jeong