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Question: How fold change is calculated in Ballgown?
0
gravatar for Ir
22 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!

ADD COMMENTlink modified 22 months ago • written 22 months ago by Ir0

Is KO & WT the covariate considered during stattest

ADD REPLYlink written 8 months ago by ag1805x10
0
gravatar for Alyssa Frazee
22 months ago by
Alyssa Frazee200
San Francisco, CA, USA
Alyssa Frazee200 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 22 months ago by Alyssa Frazee200
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 8 months ago by ag1805x10
0
gravatar for Ir
22 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 ?


 

ADD COMMENTlink modified 22 months ago • written 22 months 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 22 months ago by Alyssa Frazee200
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