voom
voomWithQualityWeights
voom
and arrayWeights
.
diffSplice
topSplice
diffSplice
.
plotSplice
diffSplice
.
plotExons
Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47. http://nar.oxfordjournals.org/content/43/7/e47
voom
accepts DGEList objects and normalization factors from edgeR.01.Introduction, 02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel, 08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq