I am running combat_met on a dataset with 43 samples and 2 conditions. The M-value matrix has 889341 probes and 43 samples. I try running combat_met
adj_bv_mat <- ComBat_met(mValues, dtype = "M-value", batch = batch, group = group, full_mod = TRUE,ncores = 4)
Found 2 batches and 43 samples. Using full model in ComBat-met.
Adjusting for 1 covariate(s) or covariate level(s). Found 6900026 missing data values Fitting the GLM model Found 19016 features with zero model variance;
these features won't be adjusted for batch effects. Errors encountered in 0 features with model fitting;
these features won't be adjusted for batch effects. Found 870325 features with zero model variance within at least one batch;
these features won't be adjusted for batch effects. Shrinkage off - using GLM estimates for parameters Error in
mu_hat_mat[, batches_ind[[jj]]] : subscript out of bounds
Any suggestions? (I have run combat_met successfully on a subset of 31 samples of this data)
Can you share the output of
str(mValues)?