The bioBakery help forum

MaAsLin for pathway analysis

Hi,

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?

Hi -

Sorry to hear that you’re experiencing these issues with MaAsLin! The lab has actually migrated to an upgraded version, which should handle irregular feature names well among other improvements (flexible normalization, transformation, and modeling choices, etc.). I’d suggest try the v2 software and see if it solves the issue.

Thanks,
Siyuan