Hello,

I have just noticed a small issue with plotMDS in limma v3.48.1 when trying to create a new MDS plot showing different dimensions, using a saved MDS object.

library(limma)

sd <- 0.3*sqrt(4/rchisq(1000,df=4))
x <- matrix(rnorm(1000*6,sd=sd),1000,6)
rownames(x) <- paste("Gene",1:1000)
x[1:50,4:6] <- x[1:50,4:6] + 2

mds1 <- plotMDS(x,  col=c(rep("black",3), rep("red",3)) )

plotMDS(mds1, dim.plot = c(3, 4), col=c(rep("black",3), rep("red",3)) )
# Error in plotMDS.MDS(mds1, dim.plot = c(3, 4), col = c(rep("black", 3),  : 
#   object 'mds' not found

I think that the problem is just that the variable mds inside the plotMDS.MDS function needs to be renamed to match the current function argument, x.

Best regards,

Jamie.

function (x, labels = NULL, pch = NULL, cex = 1, dim.plot = NULL, 
    xlab = NULL, ylab = NULL, var.explained = TRUE, ...) 
{
    if (is.null(labels) & is.null(pch)) {
        labels <- colnames(x$distance.matrix.squared)
        if (is.null(labels)) 
            labels <- 1:length(x$x)
    }
    if (is.null(dim.plot)) {
        dim.plot <- x$dim.plot
    }
    else {
        if (!identical(dim.plot, x$dim.plot)) {
            x$dim.plot <- dim.plot
            lambda <- pmax(x$eigen.values, 0)
            i <- dim.plot[1]
            mds$x <- mds$eigen.vectors[, i] * sqrt(lambda[i])
            if (lambda[i] < 1e-13) 
                warning("dimension ", i, " is degenerate or all zero")
            i <- dim.plot[2]
            mds$y <- mds$eigen.vectors[, i] * sqrt(lambda[i])
            if (lambda[i] < 1e-13) 
                warning("dimension ", i, " is degenerate or all zero")
        }
    }

 # etc.

sessionInfo()
# R version 4.1.0 (2021-05-18)
# Platform: x86_64-apple-darwin17.0 (64-bit)
# Running under: macOS Mojave 10.14.6
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
# 
# locale:
#   [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] limma_3.48.1
# 
# loaded via a namespace (and not attached):
#   [1] compiler_4.1.0 tools_4.1.0

Thanks for the heads-up, now fixed.