hi
i ran qPCR today, looking at gene 1 and housekeeping gene in a single qPCR plate. In this one plate, i ran all 3 biological replicates, ie: 3 biological replicates of condition, 3 biological replicates of control. AND for each of these biological replicates, i use 3 technical replicates for gene 1 and housekeeping gene.
How do i best analyse the data? i mean i can look at control 1 vs compressed 1, control 1 vs compressed 2, control 2 vs compressed 2 etc. so many ways to pair them up. Is there a right way to 'average' out all these to determine statistical significance?
With only 3 replicates, there is no relevant statistical tests you can apply. However, it is commonly accepted. People usually perform ANOVA or t-test. If you have multiple genes, you can correct your p-values with Bonferroni or Benjamini-Hochberg.
For microarray analysis or RNA-seq (with thousands of genes), there is the model limma that is widely used and very robust.
https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
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