Dear Arne Smits and Wolfgang Huber,
First, Thank you for your amazing package it really helps me a lot to easily perform the kind of analysis that I was looking for.
But there is one thing that I would like to know, is there a way to perform the missing value imputation in a group wise manner, just like it is possible in the Perseus analysis software?
The reason why I need this is that I am analysing co-IP mass spec data for two different animal conditions compared to control with three replicates each. The difficulty here is that the control is an empty bead without antibody, leading to rather expected missing values. So I would like to do a group-wise imputation to keep the separate conditions clear.