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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

Home Page:http://lcolladotor.github.io/derfinder

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How Fstats are generated in analyzeChr()

MonicaVara opened this issue · comments

commented

Hi,

I am using derfinder to compare two groups of samples (31 vs 17) and I want to optimize (and understand) my statistics. However, it is not clear to me how this is built in analyzeChr().

As it is based on F-modelling, is cutoffFstat the alpha or the Fstat threshold itself?

In the example I also see that when you switch from theoretical to empirical the cutoffFstat switches from 1-08 to 0.99, and I don't understand why.

Additionally, I would like to know which statistical method is used to calculate FWER, as I cannot find it anywhere.

Could you clarify all these aspects to me, please?

Thank you in advance.

Mónica

commented

Hi Mónica,

When comparing two groups of samples you will end up calculating t-statistics instead of F-statistics. The argument cutoffFstat is by default the alpha given that cutoffType = 'theoretical' by default. If you change cutoffType = 'manual' then cutoffFstat is the actual threshold.

The example is a very small subset of data with not that strong of a signal, that is why I use 0.99 there. It's just for showing how to use the functions, not a real application. The actual applications are at http://leekgroup.github.io/derSoftware/ which is the supplementary website for the derfinder paper. See bioRxiv for the pre-print.

For the FWER method, check the this paper as well as the bioRxiv pre-print. Basically, we compare the observed areas against the maximum area per permutation to control the FWER.

Best,
Leonardo