fitLogNormal: Computes a log-normal linear model and permutation based p-values.
Description
Wrapper to perform the permutation test on the t-statistic. This is the original
method employed by metastats (for non-sparse large samples). We include CSS normalization
though (optional) and log2 transform the data. In this method the null distribution is not assumed to be a t-dist.
Usage
fitLogNormal(obj, mod, useCSSoffset = TRUE, B = 1000, coef = 2, sl = 1000)
Arguments
obj
A MRexperiment object with count data.
mod
The model for the count distribution.
useCSSoffset
Boolean, whether to include the default scaling
parameters in the model or not.
coef
The coefficient of interest.
sl
The value to scale by (default=1000).
Value
Call made, fit object from lmFit, t-statistics and p-values for each feature.