I have 8 samples. 4 control and 4 treated. I can obtain a within sample dispersion estimate if I make a dds object using only the control samples.
condition <- factor(c(rep("Control1", 2), rep("Control2", 2)))
And obtain dispersion estimate from this WITHIN group comparison.
I would like to use the dispersion estimates obtained from this WITHIN group comparison and apply it to the BETWEEN group comparison
condition <- factor(c(rep("Control", 4), rep("Treatment", 4)))
in order to perform differential expression analysis on the BETWEEN group comparison using the WITHIN group dispersion estimate.
Can someone tell me how to accomplish this.