I ran deseq on 8 samples, which took about 30-45mins. But on running results(), it's been more than 3 hours and still running. I can hear my laptop buzzing.
dd_cc1=DESeq(dds_CC) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing res.cc=results(dds_cc1,contrast = c("sex","male","female")) sessionInfo( )
It ran faster if I filtered the table based on reads. So it works, but it's just being slow with larger datasets