[R] Significance testing for paired counts data with small sample size and some genuine zero values

[michael watson (IAH-C)]

Dear All

I will try and keep this succinct!  The data is counts of a particular
molecule in different cell types taken from the same 5 subjects.  The
data are paired as they come from the same subject.  The aim is to
determine whether the cell types differ in terms of the abundance of
each of the molecules.

I first thought of a paired two-sample t-test for each pairing of cell
types, but cannot log the data due to the presence of zero values.

Next was the idea of the wilcoxon signed-rank test, but that would not
work with such small sample sizes.

Two questions:

1) what is the best way to analyse these data?
2) (more general) what is the best approach when one wishes to log
counts data that contains genuine zero values?

Many thanks
Mick

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