limma powers differential expression analyses for RNA-sequencing and microarray studies
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Cites methods from "limma powers differential expressio..."
...249 The di erential expression was calculated using limma [8]....
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Cites methods from "limma powers differential expressio..."
...The limma package provides the removeBatchEffect function [7], which fits a linear model containing a blocking term for the batch structure to the expression values for each gene....
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...The differential expression analysis was performed using methods from the limma package [7]....
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1,420 citations
Cites methods from "limma powers differential expressio..."
...featureCounts produces a matrix of genewise counts suitable for input to gene expression analysis packages such as limma (13), edgeR (15) or DESeq2 (16)....
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...Bioconductor contains many highly cited packages for the analysis of RNA-seq read counts, including limma (13,14), edgeR (15) and DESeq2 (16) for differential expression analyses and DEXSeq (4) for analysis of differential splicing....
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"limma powers differential expressio..." refers background in this paper
...Users can control either the family-wise type I error rate or the false discovery rate (46)....
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"limma powers differential expressio..." refers methods in this paper
...Such a plot is called a Bland-Altman plot [36] or a Tukey mean-difference plot [10]....
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