I have been having an error showing this:
69 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
so I replaced the code with this:
dds <- DESeqDataSetFromMatrix(countData=cells2, colData = info2, design = m1) dds <- estimateSizeFactors(dds) nc <- counts(dds, normalized=TRUE) filter <- rowSums(nc >= 10) >= 2 dds <- dds[filter,] dds <- estimateDispersions(dds) dds <- nbinomWaldTest(dds, maxit=5000000000, modelMatrix=m1)
I have still been getting rows that don't converge that is why my maxit reached this big. Is this big maxit okay? Anyway, so I don't get the error anymore on rows not converging but I get this warning message instead:
In fitBeta(ySEXP = ySEXP, xSEXP = xSEXP, nfSEXP = nfSEXP, alpha_hatSEXP = alpha_hatSEXP, : NAs introduced by coercion to integer range
I tried to search online but couldn't find a similar warning. What does this mean? Should I change anything or I can proceed with my analysis?