limma: correct design matrix and topTable for 2 way comparison

Question

[erica.fary]

Dear All,

A naive question, but I am facing an issue regarding the design matrix and the intercept when conducting differential expression analysis within the limma/edge framework. And then how to set the "coef" in TopTable accordingly.

I would like to do a simple DE analysis between 2 groups (cond1, cond2) from gene expression matrices (cond1_dt and cond2_dt, respectively; cond12_dt being cbind of the two - both have same genes in rows)

Could someone explain me the differences among the 6 "res_de_1/2a/b/c" result tables here below ? And most importantly what would be the best way to proceed ?

cond12_dt <- cond12_dt[,c(colnames(cond1_dt), colnames(cond2_dt))]

sub_labs <- factor(c(rep(cond1, ncol(cond1_dt)),rep(cond2, ncol(cond2_dt))), levels=c(cond1, cond2))
design <- model.matrix(~ sub_labs)
v <- voom(cond12_dt, design, plot=FALSE)
fit <- lmFit(v, design)
eb_fit <- eBayes(fit)
res_de_1a <- topTable(eb_fit,  adjust.method="BH", coef=ncol(v$design), number=Inf, sort.by="p")
res_de_1b <- topTable(eb_fit,  adjust.method="BH", number=Inf, sort.by="p")
res_de_1c <- topTable(eb_fit,  adjust.method="BH", coef=1, number=Inf, sort.by="p")

sub_labs <- factor(c(rep(cond1, ncol(cond1_dt)),rep(cond2, ncol(cond2_dt))), levels=c(cond1, cond2))
design <- model.matrix(~ 0+sub_labs)
v <- voom(cond12_dt, design, plot=FALSE)
fit <- lmFit(v, design)
eb_fit <- eBayes(fit)
res_de_2a <- topTable(eb_fit,  adjust.method="BH", coef=ncol(v$design), number=Inf, sort.by="p")
res_de_2b <- topTable(eb_fit,  adjust.method="BH", number=Inf)
res_de_2c <- topTable(eb_fit,  adjust.method="BH", coef=1, number=Inf)


# res_de_1b = res_de_1a
# res_de_1c similar but not equal res_de_2a
# res_de_1c similar = res_de_2b (with 2 cols)
# res_de_1c = res_de_2c

I would be grateful if anyone could help

thanks in advance

erica