Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE

Hi, I'd like to estimate the zinbwave weights to use in a differential expression analysis. Some of my tests fail with this error:

Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE Calls: DESeq ... estimateDispersionsGeneEst -> getAndCheckWeights -> stopifnot Execution halted

I tried to debug using the function getAndCheckWeights

if ("weights" %in% assayNames(object)) {
        useWeights <- TRUE
        weights <- unname(assays(object)[["weights"]])
        stopifnot(all(weights >= 0))
        weights <- weights/apply(weights, 1, max)
        if (is.null(attr(object, "weightsOK"))) {
            m <- ncol(modelMatrix)
            full.rank <- qr(modelMatrix)$rank == m
            weights.ok <- logical(nrow(weights))
            if (full.rank) {
                for (i in seq_len(nrow(weights))) {
                  weights.ok[i] <- qr(weights[i, ] * modelMatrix)$rank == 
                    m
                }
            }
            else {
                weights.ok <- rep(TRUE, nrow(weights))
                for (j in seq_len(ncol(modelMatrix))) {
                  num.zero <- colSums(t(weights) * modelMatrix[, 
                    j] == 0)
                  weights.ok <- weights.ok & (num.zero != nrow(modelMatrix))
                }
            }
            stopifnot(all(weights.ok))
        }

and lucky me, I have only one weight.ok which is false! which(!weights.ok)

[1] 29

Can you give me a hint on what I should do to fix that? I am using a 1000 x 4755 object (top 1000 variable genes) k=10 epsilon=1000

zinb <- zinbwave(se.vars, K=10, epsilon=1000, BPPARAM=BiocParallel::MulticoreParam(10)) dds <- DESeqDataSet(zinb, design = ~pool+cell.type)

estimating size factors estimating dispersions gene-wise dispersion estimates Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE Calls: DESeq ... estimateDispersionsGeneEst -> getAndCheckWeights -> stopifnot Execution halted

thanks!

drisso / zinbwave

Error in getAndCheckWeights(object, modelMatrix) : all(weights.ok) is not TRUE #39