[Feature Request] Missing medianOfRatios normalization documenation

[bvenn]

A proper documentation of the medianOfRatios normalization should be added. From a mathematical perspective the calculation of the geometric mean as the nth square root of the product of all values (1) seems odd, but when displayed as mean of the log-transformed data (2) it becomes clear, that the geometric mean is just an outlier-insensitive measure of the mean, which is intuitive to do when dealing with biological data. No prior log-transform has to be applied before normalizing the data with this method. If required a log transform can be applied to the normalized values to restore homoscedasticity.

In short, you determine the (antilog of the (mean of the (values in log space)))!

1. 
2. 

[bvenn]

It may be beneficial to implement a second version of the median of ratios (mor) normalization method, that works on log transformed data. When the data is already log transformed to reduce heteroscedasticity, a normalization does not require a geometric mean, but a standard arithmetic mean.

The additional log transform in the default mor would stabilize the values disproportionately and therefore the resulting differencial normalization would be non-sufficient.

[bvenn]

Additionally, it would be great to have access to the applied scaling factors to check the validity of the normalization!