I came across a problem with glimmaMA() that took me a while to figure out. I've been using it successfully for a while but my latest experiment using almost the same code would just produce blank plots with no error message. The only difference in the code was it was a non-model organism so I pulled annotation information from NCBI's gtf file, which has the symbols in a column named "gene". This turns out to cause some internal problem in glimmaMA() that tries to put the rownames into a column named "gene" in the bottom table. No error is given, just a blank plot. glimmaMDS() is not affected. Below is a reproducible example. On a happy note, I first noticed this problem with R 4.0.3 so this forced me to update to 4.1.0/BioC 3.13 more quickly than I usually do!

library(Glimma)
library(limma)
library(edgeR)

dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma"))

#This works:
glimmaMDS(dge)

design <- readRDS(
  system.file("RNAseq123/design.rds", package = "Glimma"))
contr.matrix <- readRDS(
  system.file("RNAseq123/contr.matrix.rds", package = "Glimma"))

v <- voom(dge, design)
vfit <- lmFit(v, design)
vfit <- contrasts.fit(vfit, contrasts = contr.matrix)
efit <- eBayes(vfit)

#This works:
glimmaMA(efit, dge = dge)

#Change SYMBOL column name to "gene"

names(dge$genes)[2] <- "gene"
names(efit$genes)[2] <- "gene"

#This still works:
glimmaMDS(dge)

#This does not:
glimmaMA(efit, dge = dge)
#Just a blank plot with no errors

sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] edgeR_3.34.0 limma_3.48.0 Glimma_2.2.0

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.4.0        Biobase_2.52.0              httr_1.4.2                 
 [4] jsonlite_1.7.2              bit64_4.0.5                 splines_4.1.0              
 [7] assertthat_0.2.1            stats4_4.1.0                blob_1.2.1                 
[10] GenomeInfoDbData_1.2.6      yaml_2.2.1                  pillar_1.6.1               
[13] RSQLite_2.2.7               lattice_0.20-44             glue_1.4.2                 
[16] digest_0.6.27               GenomicRanges_1.44.0        RColorBrewer_1.1-2         
[19] XVector_0.32.0              colorspace_2.0-1            htmltools_0.5.1.1          
[22] Matrix_1.3-3                DESeq2_1.32.0               XML_3.99-0.6               
[25] pkgconfig_2.0.3             genefilter_1.74.0           zlibbioc_1.38.0            
[28] purrr_0.3.4                 xtable_1.8-4                scales_1.1.1               
[31] BiocParallel_1.26.0         tibble_3.1.2                annotate_1.70.0            
[34] KEGGREST_1.32.0             generics_0.1.0              IRanges_2.26.0             
[37] ggplot2_3.3.3               ellipsis_0.3.2              cachem_1.0.5               
[40] SummarizedExperiment_1.22.0 BiocGenerics_0.38.0         survival_3.2-11            
[43] magrittr_2.0.1              crayon_1.4.1                memoise_2.0.0              
[46] evaluate_0.14               fansi_0.4.2                 tools_4.1.0                
[49] lifecycle_1.0.0             matrixStats_0.58.0          S4Vectors_0.30.0           
[52] locfit_1.5-9.4              munsell_0.5.0               DelayedArray_0.18.0        
[55] AnnotationDbi_1.54.0        Biostrings_2.60.0           compiler_4.1.0             
[58] GenomeInfoDb_1.28.0         tinytex_0.31                rlang_0.4.11               
[61] grid_4.1.0                  RCurl_1.98-1.3              rstudioapi_0.13            
[64] htmlwidgets_1.5.3           bitops_1.0-7                rmarkdown_2.8              
[67] gtable_0.3.0                DBI_1.1.1                   R6_2.5.0                   
[70] knitr_1.33                  dplyr_1.0.6                 fastmap_1.1.0              
[73] bit_4.0.4                   utf8_1.2.1                  parallel_4.1.0             
[76] Rcpp_1.0.6                  vctrs_0.3.8                 geneplotter_1.70.0         
[79] png_0.1-7                   tidyselect_1.1.1            xfun_0.23