Question: How fold change is calculated in Ballgown?
gravatar for Ir
7 days ago by
Ir0 wrote:


I would like to clarify how Ballgown computes the fold change (FC)?

If "group" is defined as c('KO','WT'), what value goes to numerator, and what to denominator?  FC= KO/WT   or FC=WT/KO

pData(bg) = data.frame(id=sampleNames(bg), group=rep(c('KO', 'WT')

FC= ?

Thank you!

ADD COMMENTlink modified 4 days ago • written 7 days ago by Ir0
gravatar for Alyssa Frazee
6 days ago by
Alyssa Frazee100
San Francisco, CA, USA
Alyssa Frazee100 wrote:

"KO" will be used as the reference group (denominator) here, so the fold change is calculated as WT / KO.

(It's similar to the situation where you use the `lm` function in R with `group` as a covariate: KO would be the baseline factor level because it comes first alphabetically). 

ADD COMMENTlink written 6 days ago by Alyssa Frazee100
gravatar for Ir
4 days ago by
Ir0 wrote:

Just to clarify if I missed this info in the manual, so it means that this is a default  (WT/KO) and I can not control nominator and denominator ?


ADD COMMENTlink modified 3 days ago • written 4 days ago by Ir0

Correct: you can't control which is the numerator and which is the denominator. If you want KO in the numerator and WT in the denominator, you can take the reciprocal after doing stattest. 

ADD REPLYlink written 2 days ago by Alyssa Frazee100
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