I have a question regarding technical replicates of the same biological sample.
I have for a sample the following:
sample1-rep1 sample1-rep2 Sample2-rep1 Sample2-rep2 etc up to 12
The individual samples are biological replicates while the the sample (rep1 and 2) are technical replicates from the same tissue.
My question is, for DESeq2, should this cause issues for normalization/VST transformation? I primarily need the normalize counts/vst transformed counts for further downstream analysis (not DE)
for my model effect, batch is treated according to when library preps took place.
please note, i do not intend to collapse technical replicates.