Question: DEXseq with technical replicates
gravatar for chipolino
15 months ago by
chipolino0 wrote:

Hi everyone,

I want to do differential exon usage analysis with DEXseq. I have 3 affected (2 technical replicates for each individual, so 6 samples total) and 3 unaffected individuals  (also 2 technical reps for each sample, 6 samples overall). My question is how should I take into account technical replicates in this experiment with DEXseq? Should I add it in the formula somehow? And how my metadata table should look like in this case?

Thank you!

dexseq • 230 views
ADD COMMENTlink modified 15 months ago by Alejandro Reyes1.7k • written 15 months ago by chipolino0
Answer: DEXseq with technical replicates
gravatar for Alejandro Reyes
15 months ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:

Hi g.e.novakowsky, 

The DEXSeq model considers two sources of variation, (1) biological, which is estimated from biological replicates and (2) technical, which is small compared to biological variability, follows a Poisson distribution and can be estimated directly from the mean (see for example: It is therefore recommended to collapse technical replicates in the DEXSeq analysis: this will give you more sequencing depth for each biological sample that translates in more power in the tests.


ADD COMMENTlink written 15 months ago by Alejandro Reyes1.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 238 users visited in the last hour