I am currently analyzing with DESeq2 a group 32 ovine tumors against 3 healthy controls. 80% of the tumor samples are technical replicates. I tested the DESeq analysis with or without using the function collapseReplicates(dds, groupby= colData(dds)$Sample, renameCols=T).
In both cases the MA plot had a weird shape looking like this (+PCA and dispersion plots):
Moreover, 272 (for the no collapsing condition) and 695 (for the collapsing condition) genes have been flagged as outliers.
I have already done other DESeq analysis with the same code on smaller datasets and never seen such distribution. Could someone tell me if this is a normal distribution for tumor samples or for this amount of samples? If not, what can be the reasons and what can I do?
Thanks in advance!