how should I understand the coef=1 in limma

0

Entering edit mode

linouhao ▴ 20

@linouhao-15901

Last seen 20 months ago

United States

when I toptable the fit in limma, and set coef=1, the pvalue and padj are all 0, and coef=2 seems to be the right result, how should I understand coef=1, does it mean the control group compared to the null hypothesis ? thanks a lot

limma • 1.1k views

ADD COMMENT • link 4.3 years ago linouhao ▴ 20

1

Entering edit mode

That depends on what are your comparisons, it is simply used to extract the values of the comparisons. Without knowing how did you design the experiment and defined the comparisons we can only guess.

ADD REPLY • link 4.3 years ago Lluís Revilla Sancho ▴ 760

0

Entering edit mode

thanks a lot. here is the code

library(CLL)
data(sCLLex)
library(limma)
design=model.matrix(~factor(sCLLex$Disease))
fit=lmFit(sCLLex,design)
fit=eBayes(fit)
options(digits = 4)
topTable(fit,coef=2,adjust='BH')

https://ibb.co/x3gWM6y

I am also puzzuled whether the following is right? https://ibb.co/9cPtWWt

ADD REPLY • link 4.3 years ago linouhao ▴ 20

Login before adding your answer.