I performed an RNAseq experiment for two conditions, with 4 biological replicates for Condition 1 and 2 biological replicates for Condition 2.
Furthermore, I have three technical replicates for 2 of the biological replicates in Condition 1, and no technical replicates for the other two biological replicates of Condition 1 (only one instance of each).
For Condition 2, biological replicate 1 had two technical replicates, while biological replicate 2 had three technical replicates.
Will this un-evenness in replicates (both technical and biological) affect the downstream analysis?
I am using DESeq2 and collapsing technical replicates by adding the raw counts into a single sample, as explained in the DESeq manual.
Any input is appreciated. Thank you.