DE analysis using technical replicates

Question

[vin23]

Hello all, I am performing a differential expression analysis of a dataset for Th cells. The dataset contains technical replicate samples. I have tried dropping a single replicate sample or averaging it out and consider them as one sample. Can anyone suggest an approach to deal with technical replicates. Thank you

Answer 1

[swbarnes2]

You can just sum up the counts of technical replicates. No need to average or remove.

[vin23]

I have two groups, one group contains replicates while the other does not. So is it okay sum up only replicates of one group.

[ATpoint]

Yes, it will result in depth differences that will be handled by the normalization step. That assumes that technical means something like multiple sequencing runs of the same sample.

[vin23]

Okay Thank you so much for the explanation