glMDPlot output empty html

[u9090]

Hi,

Trying to run this example code, but outputs an empty html file (about 993 b), along with the 'css' and 'js' folders:

library(limma)
library(edgeR)

data(lymphomaRNAseq)
x <- lymphomaRNAseq

sel <- rowSums(cpm(x$counts)>0.5)>=3
x <- x[sel,]

genotype <- relevel(x$samples$group, "Smchd1-null")
x <- calcNormFactors(x, method="TMM")
des <- model.matrix(~genotype)

## Apply voom with sample quality weights and fit linear model
v <- voomWithQualityWeights(x, design=des, normalization="none", plot=FALSE)
vfit <- lmFit(v,des)

## Apply treat relative to a fold-change of 1.5
vtfit <- treat(vfit,lfc=log2(1.5))
vfit <- eBayes(vfit)
results <- decideTests(vfit,p.value=0.01)

glMDPlot(vfit, counts=x$counts, anno=x$genes, groups=genotype, samples=1:7,
         status=results[,2], main="MD plot: Wild-type vs Smchd1",
         display.columns=c("Symbols", "GeneID", "GeneName"),
         folder="Smchd1-Lymphoma")

My sessionInfo():

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux release 6.2 (Carbon)

locale:
 [1] LC_CTYPE=C          LC_NUMERIC=C        LC_TIME=fr_FR       LC_COLLATE=C        LC_MONETARY=C       LC_MESSAGES=C       LC_PAPER=C
 [8] LC_NAME=C           LC_ADDRESS=C        LC_TELEPHONE=C      LC_MEASUREMENT=C    LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ggrepel_0.8.0        ggplot2_3.1.0        gplots_3.0.1         RColorBrewer_1.1-2   dplyr_0.7.7          Glimma_1.10.0
 [7] edgeR_3.20.9         limma_3.34.9         org.Hs.eg.db_3.5.0   AnnotationDbi_1.42.1 IRanges_2.15.17      S4Vectors_0.19.19
[13] Biobase_2.38.0       BiocGenerics_0.27.1  tibble_1.4.2         data.table_1.11.8    RevoUtils_10.0.8     RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19       locfit_1.5-9.1     lattice_0.20-35    prettyunits_1.0.2  ps_1.2.0           gtools_3.8.1       assertthat_0.2.0
 [8] rprojroot_1.3-2    digest_0.6.18      R6_2.3.0           plyr_1.8.4         backports_1.1.2    RSQLite_2.1.1      pillar_1.3.0
[15] rlang_0.3.0.1      curl_3.2           lazyeval_0.2.1     gdata_2.18.0       callr_3.0.0        blob_1.1.1         desc_1.2.0
[22] devtools_2.0.1     bit_1.1-14         munsell_0.5.0      compiler_3.4.3     pkgconfig_2.0.2    base64enc_0.1-3    pkgbuild_1.0.2
[29] tidyselect_0.2.5   crayon_1.3.4       withr_2.1.2        bitops_1.0-6       grid_3.4.3         jsonlite_1.5       gtable_0.2.0
[36] DBI_1.0.0          magrittr_1.5       scales_1.0.0       KernSmooth_2.23-15 cli_1.0.1          debugme_1.1.0      fs_1.2.6
[43] remotes_2.0.1      testthat_2.0.1     bindrcpp_0.2.2     tools_3.4.3        bit64_0.9-7        glue_1.3.0         purrr_0.2.5
[50] processx_3.2.0     pkgload_1.0.1      colorspace_1.3-2   sessioninfo_1.1.0  caTools_1.17.1.1   memoise_1.1.0      bindr_0.1.1
[57] usethis_1.4.0

Have you already encountered this error before?

Thanks !

[Shians]

Thanks for the bug report. Running the code gives me a html of 968b that displays as expected in Safari and Chrome on macOS. Which browser are you using? You may need to dig into the inspector to see what error messages have popped up there.

[u9090]

I tried Safari and Firefox on mac. What do you mean by the "inspector"? I don't have any error messages from the std error.

[Shians]

See here. Inside the inspector click "Console" which should display some errors.

[u9090]

Problem solved with Inspector. Thanks !

[Shians]

No problem.