Cryptic error for multiple testing correction

[rbutleriii]

Hi, I have multiple sets of gene lists and am running pairwise enrichment using the following function on them:

# function runs enrichment and saves to file for p and padj
# takes two set lists, background gene count and output name and pdf width
enrich = function(list1, list2, background, outname, width=7) {
  # enrichment basic
  gom.obj = newGOM(list1, list2, background)
  pdf(file=paste0(today, nameset, outname, ".pdf"), width=width)
  drawHeatmap(gom.obj, grid.col="Blues")
  dev.off()
  # enrichment multiple testing correction
  pdf(file=paste0(today, nameset, outname, "_padj.pdf"), width=width)
  drawHeatmap(gom.obj, grid.col="Blues", adj.p=T)
  dev.off()
}

Usually works fine, but on one comparison (5 sets x 6 sets), I get three enrichments with the standard Heatmap (0.031, 6e-03, 6e-03), but a cryptic error and a blank pdf for the multiple testing set:

Error in (function (side, at = NULL, labels = TRUE, tick = TRUE, line = NA,  :
  no locations are finite

Am I correct in thinking this means none of the enrichments remained after multiple correction? Could it return an error as such?

[adomingues]

Hi @rbutleriii,

I am not sure if you found a solution for your problem, but I encountered the issue just now and it is an heatmap.2 issue if all values in the matrix are the same (e.g. if all padj.values are 1).

Reproducible example:

library("gplots")
plot.mat <- matrix(rep(1, 6), , nrow = 3, ncol = 2, dimnames = list(letters[1:3], letters[4:5]))
heatmap.2(plot.mat)

plot.mat <- matrix(rep(0.5, 6), , nrow = 3, ncol = 2, dimnames = list(letters[1:3], letters[4:5]))
heatmap.2(plot.mat)

# replace any number
plot.mat[1, 2] <- 0.01
heatmap.2(plot.mat)

I will try to add an error message for next release.

Thank you for reporting.