Handling NA values in limma's voom design matrix
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Entering edit mode
3 months ago
rubic ▴ 240

Hi, I'm trying to use limma's voom for RNA-seq data, where my design matrix contains NA values. Can voom handle these NAs or is the only solution to toss out the samples with these NAs?

Here's my example data:

set.seed(1)
counts.mat <- matrix(as.integer(runif(1000*10, 10,1000)),nrow = 1000, ncol = 10, dimnames = list(paste0("g",1:1000),paste0("s",1:10)))
design.df <- data.frame(id = paste0("s",1:10),
                        sex = sample(c("female","male"), 10, replace = T),
                        age = sample(c(5, 7, 10), 10, replace = T))
#adding NAs
design.df$sex[3] <- NA
design.df$age[5] <- NA

design.mat <- model.matrix(~ id + age + sex, model.frame(~ ., design.df, na.action = na.pass))
dge <- edgeR::DGEList(counts = counts.mat)
dge <- edgeR::calcNormFactors(dge)
voom.obj <- limma::voom(dge, design.mat, plot=TRUE)

The last last gives this error message:

Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)
rna-seq voom design.matrix limma NA • 263 views
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1
Entering edit mode
3 months ago

Cross-posted and answered by the limma developer: https://support.bioconductor.org/p/9144237/

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