Hello, I am currently trying to do a sample size estimation for an RNAseq experiment I am planning, using ssizeRNA package in R. This package uses average read counts and dispersion, proportion of DEGs and total genes mapped to estimate sample size based on power. Here is a link to the vignette (https://cran.r-project.org/web/packages/ssizeRNA/vignettes/ssizeRNA.pdf). I used a publically available dataset somewhat related to my topic/tissue of interest to estimate the parameters needed, similar to what they did in the last part of the vignette.
However, I am getting really high numbers per group (400+) . I am not sure if I am doing it right and not many people seem to estimate sample sizes prior to RNAseq experiments. I also noticed that RNAseq papers done in humans use relatively high number of samples per group however, nothing as high as what the analysis gave me. Has anyone used this package before? And are there any tips you can give? Or are there other tools/packages/websites that you can recommend for this? Thanks
The important question is whether you can afford to acquire this many samples. 400 samples per group, say 2 groups will be 800 and this will cost you more than 100.000$. Typically for clinical studies you do as many as you can get your hands on while respecting the budget obviously, and for mouse (or similar) studies one typically goes much lower, as budget is often limited. Can you give some context? What experiment is planned?
Hey thanks for your response. We are performing RNAseq in umbilical cord blood PBMCs of preterm babies. The premise is to see if in vitro treatment of umbilical cord PBMCs with steroids correlates with antenatal corticosteroid efficacy. We want to identify differential transcriptomic profiles in PBMC samples of babies who respond and those who do not. For each sample, we'll treat cells in vitro with LPS or LPS+DEX. Our budget will not be sufficient for 100+ samples and also timeframe for collecting samples is not feasible with my thesis timeline either. I just find it strange that we need so many samples to achieve statistical power/significance and I am wondering if it is an issue with my ssizeRNA analysis instead. I personally haven't seen many transcriptomics papers in human PBMCs with 400+ samples. That's why I'm a little baffled.