**90**wrote:

Hello,

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.

TIA.