How-to: run a differential expression analysis
Running DESeq2
For comprehensive tutorials, see here:
Running edgeR
Running basic DE
calc_DE <- function(X, f.a, filt, group){
X = X[f.a,filt]
group = group[filt]
if( sum(group==1) < 2 ) {
m.X1 = (X[,group==1])
} else {
m.X1 = rowMeans(X[,group==1])
}
if( sum(group==2) < 2 ) {
m.X2 = (X[,group==2])
} else {
m.X2 = rowMeans(X[,group==2])
}
m.X = rowMeans(X)
fc = log2(m.X1/m.X2)
X.ps_g = sapply(1:dim(X)[1], function(k) wilcox.test(X[k,group==1], X[k,group==2], alt="g")$p.val)
X.padj_g = p.adjust(X.ps_g , method = "BH")
X.ps_l = sapply(1:dim(X)[1], function(k) wilcox.test(X[k,group==1], X[k,group==2], alt="l")$p.val)
X.padj_l = p.adjust(X.ps_l , method = "BH")
X.ps = sapply(1:dim(X)[1], function(k) wilcox.test(X[k,group==1], X[k,group==2])$p.val)
X.padj = p.adjust(X.ps , method = "BH")
de = cbind(m.X, fc, X.ps_g, X.padj_g, X.ps_l, X.padj_l, X.ps, X.padj, m.X1, m.X2)
return(de)
}
deg = calc_DE(cpm, keep, subset, groups )
