Question: How fold change is calculated in Ballgown?
0
2.6 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 • 1.5k views
modified 2.6 years ago • written 2.6 years ago by Ir0

Is KO & WT the covariate considered during stattest

Answer: How fold change is calculated in Ballgown?
0
2.6 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).

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.

Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically,

correct?

thank you

Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically,

correct?

thank you

Answer: How fold change is calculated in Ballgown?
0
2.6 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 ?