How fold change is calculated in Ballgown?
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Ir • 0
@ir-11113
Last seen 7.2 years ago

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 • 3.4k views
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Is KO & WT the covariate considered during stattest

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Alyssa Frazee ▴ 210
@alyssa-frazee-6710
Last seen 3.4 years ago
San Francisco, CA, USA

"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). 

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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. 

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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

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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

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Ir • 0
@ir-11113
Last seen 7.2 years ago

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 ?


 

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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. 

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