I am using DEXSeq to compare exons within two conditions. The applied strategy was the same as in tutorial.
However, after running testForDEU(...) function the following messages were reported:
using supplied model matrix
5 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
I tried to set maxit value, however this did not work:
Error in testForDEU(dxdFull, maxit = 500) : unused argument (maxit = 500)
Afterwards I tried to run next step and got many warning messages:
Fit for gene/exon ENSG00000241769.3+ENSG00000241489.3+ENSG00000010404.13+ENSG00000238039.1 threw the next warning(s): the matrix is either rank-deficient or indefinite
Why is this occurring? How is it possible to fix?
Also, I did not clean up the exon counts before running DEXSeq. Should I perform some filtering in advance (i.e. exclude lowly expressed genes)?