Closed TsStef closed 7 years ago
Do you get the same error on the data without subsetting to the selected surface types?
I did not get any error, when analyzing the "sampling_place" (which has just two levels). However I decided to subset the data, because there was a message:
Can't analyze currently
Probably because the factor has more than three levels. I found that line:
if(ncol(mmCount)>3){ stop("Can't analyze currently.") }
So I decided to analyze a subset of three surfaces. And then I got that error.
Maybe re-leveling the 'surface_type' column helps:
obj1 <- obj[, which(pData(obj)$surface_type %in% selected)]
pData(obj1)$surface_type <- factor(pData(obj1)$surface_type)
Thanks I will try. And could you tell the reason for the "Can't analyze currently" error? Is it the factor's levels or there is another reason?
Ok, let us know how it goes. The fitFeatureModel model is only supported for two level factor comparisons, which gives rise to the error.
Hello, I am trying to analyse differential abundances of bacterial taxa in subways. Using fitFeatureModel(). First I subset the MRexperiment object, keeping three levels of the factor "surface_type":
obj1 <- obj[, which(pData(obj)$surface_type %in% selected)]
After that I normalized the data, using default options. When fitting the model I got that error massage
But when I check for NA, I got: is.na(normFactors(obj1))
Can you, please, give me a hint where is my fault! Thank you!