Hello, I have been trying to run an analysis using Maaslin2, running the program through R Studio. I have no issues calling in the input data file (which is relative metatranscriptomic data per sample) and then the metadata (which includes, discrete, binary, and continuous variables) with NA where there is no data. The program itself starts (and the demo worked), but no matter how I try to tweak the data I keep getting errors that lead to no viable output. The error code looks like:
Error in glm.fit(x = structure(numeric(0), .Dim = c(0L, 231L), .Dimnames = list( :
object āfitā not found
In addition: Warning messages:
1: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL, :
no observations informative at iteration 1
2: glm.fit: algorithm did not converge
3: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL, :
no observations informative at iteration 1
4: glm.fit: algorithm did not converge
Edit: On readjusting the data frames, I was able to reduce the errors to:
Error in contrasts<-
(*tmp*
, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
And on review of the file, it seems for some reason it is reading the metadata file in, but it is taking the header as the āvalueā, i.e. not looking past the first line. I am unsure why this is the case, given it is a tab-delimitated formatā¦
I presume it is an issue with how it is trying to compare the two input files, but I canāt seem to figure out the issue. Any help is much appreciated!