I continuously receive this error when I try to run sva with my count data
R code for sva:
# Loading all variables library(sva) dat <- dds_matrix idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod <- model.matrix(~batch, colData(dds)) mod0 <- model.matrix(~1, colData(dds)) svseq <- svaseq(dat, mod, mod0)
I receive this error message.
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
I have very distinct batches which can be seen in this plot.
I have clearly dictated the batches as factors and this exact process has worked before. This is with a new, but very similar data set.
If it is simply not possible to remove these batch effects, how would I go about bringing these two batches closer together, they are definitely the same condition and the variance is likely due to batch effects, not biological significance.