Question: How fold change is calculated in Ballgown?
0
2.2 years ago by
Ir0
Ir0 wrote:

Hi,

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!

ballgown • 1.3k views
ADD COMMENTlink
modified 2.2 years ago • written 2.2 years ago by Ir0

Is KO & WT the covariate considered during stattest

ADD REPLYlink written 12 months ago by ag1805x10
Answer: How fold change is calculated in Ballgown?
0
2.2 years ago by
Alyssa Frazee210
San Francisco, CA, USA
Alyssa Frazee210 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 2.2 years ago by Alyssa Frazee210
1

Is any log transformation done on the FPKM values during FC calculation? I tried to manually calculate the FC by extracting the FPKM values for few genes using gexpr(), but the result I obtained differs considerably from the stattest result.

Also after stattest the genes that were supposed to be up-regulated has FC<1 and vice-versa.

ADD REPLYlink written 12 months ago by ag1805x10
Answer: How fold change is calculated in Ballgown?
0
2.2 years ago by
Ir0
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 2.2 years ago • written 2.2 years 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 2.2 years ago by Alyssa Frazee210
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