DESeq2 estimateDispersions taking infinite time
I am trying to find differentially expressed genes on a data with 1,500 samples and 26,000 genes, using the following code:
cds <- DESeqDataSetFromMatrix(counts, design.matrix, design=~condition) cds <- DESeq(cds)
But the DESeq function prints the message "gene-wise dispersion estimates" and it takes unlimited time. I have waited for the function to finish a few days. It's running on a with 512 GB RAM and 64 cpus. I tried to debug the function, it makes a call to estimateDispersions(), for which the source code does not seem available.
Any ideas?
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For that many samples you'll probably get much better performance with limma/voom. Having said that, please post this on the bioconductor support site, where Mike Love is more active (he'll probably see this too, but you'll get a faster reply there).