Description References See Also
This page gives an overview of LIMMA functions to analyze RNA-seq data.
voom
Transform RNA-seq or ChIP-seq counts to log counts per million (log-cpm) with associated precision weights. After this tranformation, RNA-seq or ChIP-seq data can be analyzed using the same functions as would be used for microarray data.
voomWithQualityWeights
Combines the functionality of voom
and arrayWeights
.
diffSplice
Test for differential exon usage between experimental conditions.
topSplice
Show a data.frame of top results from diffSplice
.
plotSplice
Plot results from diffSplice
.
plotExons
Plot logFC for individual exons for a given gene.
Law, CW, Chen, Y, Shi, W, Smyth, GK (2014). Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15, R29. http://genomebiology.com/2014/15/2/R29
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
See also the edgeR package for normalization and data summaries of RNA-seq data, as well as for alternative differential expression methods based on the negative binomial distribution.
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.