limma

This module is a partial port in Python of the R Bioconductor limma package.

References

[Sartor2006]

M.A. Sartor, C.R. Tomlinson, S.C. Wesselkamper, S. Sivaganesan, G.D. Leikauf, M. Medvedovic. 2006. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics 7(538). doi:10.1186/1471-2105-7-538

[Smyth2004]

G.K. Smyth. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3(1). doi:10.2202/1544-6115.1027

Code documentation

fitFDist(x, df1[, covariate])	Moment estimation of the parameters of a scaled F-distribution given one of the degrees of freedom.
squeezeVar(var, df[, covariate, robust, ...])	Squeeze a set of sample variances together by computing empirical Bayes posterior means This function implements empirical Bayes algorithms proposed by [Smyth2004] and [Phipson2016].