I finished running DESeq2 on my dataset that includes 6 timepoints and 3 biological replicates per timepoint. I would like to run a PCA analysis for quality assessment but am unsure which count transformation method I should use, vst or rlog.
The calculated the size factors for my dataset (below). Based on this, there does not appear to be a large variation in sequencing depth (dynamic range of size factors ≳ 4, mentioned in Love, Huber, and Anders, 2014) all the samples. However, note that K013 does have a smaller size factor compared to other samples but does not exceed a factor of 4.
sizeFactors (dds) X12HPA_J022 1.2875797 X12HPA_J024 1.7052146 X12HPA_J050 0.9460303 X1DPA_K001 1.1828260 X1DPA_K011 1.0955579 X1DPA_K121 0.7791666 X2DPA_K013 0.4708761 X2DPA_K015 1.0936920 X2DPA_K021 1.2141511 X3DPA_K012 0.7602281 X3DPA_K014 1.0525988 X3DPA_K023 0.8606639 X4DPA_K040 0.7807291 X4DPA_K080 1.0124977 X4DPA_K120 1.3053801 X5DPA_K010 0.9436090 X5DPA_K020 1.1898311 X5DPA_K030 1.1898311
In this case would it be better to use rlog and normalize for sequencing depth, or would use of vst be okay? Thanks!