Hello, I was wondering if someone could provide some advice on how to select parametric vs non-parametric analysis with the Ct values. I may be missing where to go and check if the data is normally distributed. I did the analysis both ways and it changed the profile in DE genes.
I’m also wondering if the threshold for DE is always set to 2 FC and/or if that can be adjusted. I have some genes with a p<0.05 and showing a 1.8 or 1.9 FC and I’m just wondering if it’s possible to include those as DE genes.
Thank you!
Normal distribution: this is in the Normlization step, such as boxplot and density plot;
Parametric vs non-parametric: in general, if you have enough sample size (>10 samples per group) with normalization, the parametric is usually preferred for RNAseq / qPCR
DE selection: you can adjust p-value threshold (for instance, FDR 0.1, 0.05, 0.01 are all acceptable). You can also turn off FC. However, you should be transparent (in reporting the threshold) and be consistent if you compare results from different studies.
Thank you very much for your response.