**0**wrote:

Dear all,

Let me ask you all a question.

If I want to create a volcano plot after using the treat function, What kind of parameters should I use? Of note, in this case, all genes do not rank using Log2fold change. Should I use xlab="treat.lfc" and ylab="** ? **" . Could anyone please help me?

Thanks in advance.

`> names(tfit)

"coefficients" "rank" "assign" "qr" "df.residual"

"sigma" "stdev.unscaled" "design" "correlation" "genes"

"Amean" "cov.coefficients" "contrasts" "df.prior" "s2.prior"

"s2.post" "df.total" "t" "p.value" "treat.lfc" `

>volcanoplot(tfit,coef=1)

>plot(tfit[,6],-log(tfit[,10],10),coef=1, xlab="**log2(Fold-Change)**", ylab="**-log10(P.Value)**",main="Volcano plot",cex=0.1,pch=19)

>abline(v=c(-1,1),col="blue")

>abline(h=-log(0.05,10),col="red")

Thanks in advance.

**38k**• written 23 months ago by Sanches •

**0**