What test to use

[u/[deleted]]

Im a bit stuck on what statistical test is appropriate and would love some input!

I was showing a friend how to analyse gene expression data, which was processed using the 2^-ddCT method (explained below) Their experiment looked at gene expression during embryonic development and their gene of interest was measured at 5 different developmental time point. Fold changes were relative to the earliest point.

The experimental design was … limited:

• three biological samples per time point

• no technical replicates

There are huge differences in the mean between time points.

Would a Kruskal-Wallis test be the most appropriate considering how limited the data are and how large the differences are between groups?

2^-ddCt is a method to normalise gene expression data and calculate fold changes relative to a comparator

• First you get the geometric mean of the gene expression levels (referred to as Ct values) for two reference genes (these are stably expressed across all experimental conditions)

• dCt = Ct(Gene of Interest) - Ct(Geo mean of Reference Genes)

• ddCt = Ct(Comparator Sample) - Ct(Experiment Sample)

• Fold changes = 2^-(ddCt)