Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
0
0
Entering edit mode
sorjuelal • 0
@sorjuelal-18470
Last seen 2.2 years ago

Hi,

So sometimes I forget that the design matrix I have in mind for my analysis doesn't make sense, and I run a differential analysis anyway. If I would do this with limma for example, I would get an error telling me I have non estimable parameters or something similar. Here I made the mistake running dmrseq, and it ran the analysis without problems, until I got the DMR list with the beta, stat, pval, qval columns as NAs.

I guess technically generating DMRs is independent of the design, and this is really only used to generate the permutations and assign a p-value.

Do you think it's worth adding a check for this?

dmrseq methylation • 274 views
0
Entering edit mode

Thanks for the suggestion. Yes, I do think it's worth adding a check. I will look into this.