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.