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Question: How fold change is calculated in Ballgown?
0
16 months 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!

modified 16 months ago • written 16 months ago by Ir0

Is KO & WT the covariate considered during stattest

0
16 months ago by
Alyssa Frazee170
San Francisco, CA, USA
Alyssa Frazee170 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).

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.

0
16 months 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 ?