EDIT by RamRS:
Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21455/try-to-understand-better-how-to-set-out-an-effective-sample-size-within-the-meta
Dear all,
I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R for calculating differentially expressed OTUs between two condition:
My code looks like:
MRcoefs(fit, coef = 2, group = 3, number = 143, eff = 5.5)
Here I am setting the eff argument to 5.5 because I have calculated the effectiv_size using this code:
Effective_size(fit)
which result in table of effective size for each feature (OTU), and then I got the mean of these
mean(Effective_size(fit))
which was 5.5
When I run this, it produced an error: prop outside [0,1], I understand it should be between 0-1, but why ? is not that number in eff is the mean that I calculated which bring 5.5 ? Also when I tried to run it with .5 as the document suggested as below :
MRcoefs(fit, coef = 2, group = 3, number = 143, eff = .5)
it run nicely, no error , but it produced the same OTUs as when I did not include eff, I was expecting that some OTUs will be removed as they were below this threshold
Could you please help me?