Warnings in mergeClusters

[epurdom]

I get this warning in the vignette: ce<-mergeClusters(ce,mergeMethod="adjP") Warning: Zero sample variances detected, have been offset I dont know what that refers to, but it seems ominous.

It also spits out warnings in locfdr. It would be good to figure out how to turn those off.

[epurdom]

I have now changed the code to only run the function called by user, so may make the problem not as easy to detect. But still useful to track down.

[epurdom]

No, this is a warning from limma from getBestFeatures called by mergeClusters. It happens in the first call to mergeClusters in the vignette during the ebayes call. When I set warn=2 to make error, here is the traceback

20 doWithOneRestart(return(expr), restart) 
19 withOneRestart(expr, restarts[[1L]]) 
18 withRestarts({
    .Internal(.signalCondition(simpleWarning(msg, call), msg, 
        call))
    .Internal(.dfltWarn(msg, call)) ... 
17 .signalSimpleWarning("Zero sample variances detected, have been offset", 
    quote(NULL)) 
16 warning("Zero sample variances detected, have been offset", call. = FALSE) 
15 fitFDist(var, df1 = df, covariate = covariate) 
14 squeezeVar(sigma^2, df.residual, covariate = covariate, robust = robust, 
    winsor.tail.p = winsor.tail.p) 
13 ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, 
    trend = trend, robust = robust, winsor.tail.p = winsor.tail.p) 
12 eBayes(fit2) at getFeatures.R#425
11 .testContrasts(contrastNames = x, ...) at getFeatures.R#335
10 .getBestDendroGenes(cl = cl, dendro = dendro, contrastAdj = contrastAdj, 
    fit = fitContr, fitF = fitF, ...) at getFeatures.R#225
9 .local(x, ...) 
8 getBestFeatures(x, cl, type = c("Dendro"), dendro = dendro, returnType = c("Table"), 
    contrastAdj = c("All"), number = nrow(x), p.value = 1, isCount = isCount) at AllGenerics.R#266
7 getBestFeatures(x, cl, type = c("Dendro"), dendro = dendro, returnType = c("Table"), 
    contrastAdj = c("All"), number = nrow(x), p.value = 1, isCount = isCount) at mergeClusters.R#130
6 .local(x, ...) 
5 mergeClusters(x = transform(x), cl = primaryCluster(x), dendro = x@dendro_clusters, 
    isCount = FALSE, mergeMethod = mergeMethod, ...) at AllGenerics.R#273
4 mergeClusters(x = transform(x), cl = primaryCluster(x), dendro = x@dendro_clusters, 
    isCount = FALSE, mergeMethod = mergeMethod, ...) at mergeClusters.R#237
3 .local(x, ...) 
2 mergeClusters(ce, mergeMethod = "adjP", plot = "mergeMethod") at AllGenerics.R#273
1 mergeClusters(ce, mergeMethod = "adjP", plot = "mergeMethod")