I am analysing 142 samples belonging to 6 batches. Additionally, those samples belong to 72 strains, which means that for most of the strains there are two samples.
I could fit simple models (for strain and batches for instance), but when I get to the "full" model (~batch+strain), I get the following error:
so <- sleuth_fit(so, ~strain+batch, 'full') Error in solve.default(t(X) %*% X) : system is computationally singular: reciprocal condition number = 5.2412e-19
I should point out that of the 72 strains, only 15 have samples in distinct batches. This means that most strains (57) have both samples in the same batch.
Is the error due to an unknown bug or rather to the experimental design? Does it mean that the information on batches cannot be used?
EDIT I've posted the experimental design in a gist
batch strain replica batch_1 strain_41 1 batch_4 strain_41 2 batch_1 strain_28 1 batch_4 strain_28 2 batch_1 strain_26 1 [...]