Current GitHub issues

See GitHub page for up-to-date responses to users’ questions.



Errors: Problems removing samples with NA/NaN/Inf values

variancePartition fits a regression model for each gene and drops samples that have NA/NaN/Inf values in each model fit. This is generally seamless but can cause an issue when a variable specified in the formula no longer varies within the subset of samples that are retained. Consider an example with variables for sex and age where age is NA for all males samples. Dropping samples with invalid values for variables included in the formula will retain only female samples. This will cause variancePartition to throw an error because there is now no variation in sex in the retained subset of the data. This can be resolved by removing either age or sex from the formula.

This situtation is indicated by the following errors:

  • Error: grouping factors must have > 1 sampled level

  • Error: Invalid grouping factor specification, Individual

  • Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels

  • Error in checkNlevels(reTrms\$flist, n = n, control): grouping factors must have > 1 sampled level

Errors with BiocParallel multithreading backend