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Question: DEXseq with technical replicates
0
gravatar for g.e.novakovsky
7 months ago by
g.e.novakovsky0 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 • 129 views
ADD COMMENTlink modified 7 months ago by Alejandro Reyes1.6k • written 7 months ago by g.e.novakovsky0
Answer: DEXseq with technical replicates
1
gravatar for Alejandro Reyes
7 months ago by
Alejandro Reyes1.6k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.6k 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: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527709/). 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.

Alejandro

ADD COMMENTlink written 7 months ago by Alejandro Reyes1.6k
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