Hi,

After updating to bioconductor 3.8, I have some troubles using p.vector. The command and error are:

> fit <- p.vector(edgeR_cpm_matrix, design, Q = 0.05, MT.adjust = "BH", counts=TRUE, family= negative.binomial(10));
Error in negative.binomial(10) :
  could not find function "negative.binomial"

I can also reproduce the error with (R 3.5.0):

> library(maSigPro)
> negative.binomial(10)
Error in negative.binomial(10) :
  could not find function "negative.binomial"

However ?negative.binomial works. Any idea?

Thanks

This looks like a bug in the maSigPro package. The maSigPro package imports the MASS package but not in a way that makes the negative.binomial() function available within the p.value() function. So you have to load the MASS package explicitly yourself.

Even if you load MASS though, your code doesn't look right. It isn't correct to use family="negative.binomial" with cpm values. You could try using maSigPro with log-cpm values and the default gaussian family, but I'd suggest instead using the edgeR package itself on the actual counts.

ok it is working now. Thank you for the correction.