I tried to use MaAlLin to analysis the differential pathways among three groups. And the pathway abundance file is from HuMAnN2. I prepared .pcl and .config files, but got the following error:
Error in getMsgComposer() : object ‘msg_composer’ not found
In addition: Warning messages:
1: In which(is.na(as.numeric(lItemElement))) : NAs introduced by coercion
2: In which(is.na(as.numeric(lItemElement))) : NAs introduced by coercion
Since the pathway name (also the rownames of abundance file) contains a lot of special characters, like “:”," ", “()”, i am not sure whether this will cause this error. But i tried the replace these characters with “_”, the error is still here.
Does anyone know any solutions?