I am trying to run a typical workflow for microarray differential expression. HGCC_exp_mat_transp is a 17320 gene x 48 sample matrix. I've gone through the debugger for RStudio but I'm still at a loss as to what's going on.

Here's the code:

dim(HGCC_exp_mat_transp)
[1] 17320    48

DE_fit_mes_status <- lmFit(HGCC_exp_mat_transp, design = design_mat)
  DE_fit_mes_status.reduced <- eBayes(DE_fit)
  ranked_probes <- topTable(DE_fit_mes_status.reduced, number = 17000)

I get the following error:

Removing intercept from test coefficients
Error in data.frame(logFC = M[top]) : row names contain missing values

traceback()
4: stop("row names contain missing values")
3: data.frame(logFC = M[top])
2: .topTableT(fit = fit[c("coefficients", "stdev.unscaled")], coef = coef,
       number = number, genelist = genelist, A = fit$Amean, eb = fit[ebcols],
       adjust.method = adjust.method, sort.by = sort.by, resort.by = resort.by,
       p.value = p.value, lfc = lfc, confint = confint)
1: topTable(DE_fit_mes_status.reduced, number = 17000)

Here's the session Info:

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8       
 [4] LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] clusteval_0.1              missMethyl_1.12.0          gtools_3.5.0              
 [4] GOSemSim_2.4.1             MOFAtools_0.1              sva_3.26.0                
 [7] BiocParallel_1.12.0        genefilter_1.60.0          mgcv_1.8-23               
[10] nlme_3.1-137               gProfileR_0.6.6            ggplot2_2.2.1             
[13] kernlab_0.9-26             SNFtool_2.3.0              edgeR_3.20.9              
[16] limma_3.34.9               DESeq2_1.18.1              SummarizedExperiment_1.8.1
[19] DelayedArray_0.4.1         matrixStats_0.53.1         Biobase_2.38.0            
[22] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0        IRanges_2.12.0            
[25] S4Vectors_0.16.0           BiocGenerics_0.24.0        rrcovHD_0.2-5             
[28] rrcov_1.4-3                robustbase_0.93-0         

loaded via a namespace (and not attached):
  [1] backports_1.1.2                                     Hmisc_4.1-1                                        
  [3] corrplot_0.84                                       plyr_1.8.4                                         
  [5] lazyeval_0.2.1                                      shinydashboard_0.7.0                               
  [7] heatmap.plus_1.3                                    splines_3.4.3                                      
  [9] robustHD_0.5.1                                      digest_0.6.15                                      
 [11] ExPosition_2.8.19                                   foreach_1.4.4                                      
 [13] htmltools_0.3.6                                     GO.db_3.5.0                                        
 [15] alluvial_0.1-2                                      magrittr_1.5                                       
 [17] checkmate_1.8.5                                     memoise_1.1.0                                      
 [19] cluster_2.0.7-1                                     doParallel_1.0.11                                  
 [21] readr_1.1.1                                         Biostrings_2.46.0                                  
 [23] annotate_1.56.2                                     perry_0.2.0                                        
 [25] siggenes_1.52.0                                     prettyunits_1.0.2                                  
 [27] colorspace_1.3-2                                    blob_1.1.1                                         
 [29] ggrepel_0.8.0                                       BiasedUrn_1.07                                     
 [31] dplyr_0.7.4                                         RCurl_1.95-4.10                                    
 [33] GEOquery_2.46.15                                    bindr_0.1.1                                        
 [35] survival_2.42-3                                     iterators_1.0.9                                    
 [37] glue_1.2.0                                          ruv_0.9.7                                          
 [39] registry_0.5                                        gtable_0.2.0                                       
 [41] zlibbioc_1.24.0                                     XVector_0.18.0                                     
 [43] spls_2.2-2                                          DEoptimR_1.0-8                                     
 [45] scales_0.5.0                                        pheatmap_1.0.8                                     
 [47] mvtnorm_1.0-7                                       rngtools_1.3.1                                     
 [49] DBI_1.0.0                                           Rcpp_0.12.16                                       
 [51] progress_1.1.2                                      xtable_1.8-2                                       
 [53] htmlTable_1.11.2                                    bumphunter_1.20.0                                  
 [55] foreign_0.8-70                                      bit_1.1-13                                         
 [57] mclust_5.4                                          preprocessCore_1.40.0                              
 [59] Formula_1.2-3                                       httr_1.3.1                                         
 [61] htmlwidgets_1.2                                     RColorBrewer_1.1-2                                 
 [63] acepack_1.4.1                                       pkgconfig_2.0.1                                    
 [65] reshape_0.8.7                                       XML_3.98-1.11                                      
 [67] nnet_7.3-12                                         locfit_1.5-9.1                                     
 [69] rlang_0.2.0                                         reshape2_1.4.3                                     
 [71] later_0.7.2                                         AnnotationDbi_1.40.0                               
 [73] munsell_0.4.3                                       tools_3.4.3                                        
 [75] RSQLite_2.1.1                                       pls_2.6-0                                          
 [77] stringr_1.3.1                                       yaml_2.1.19                                        
 [79] org.Hs.eg.db_3.5.0                                  knitr_1.20                                         
 [81] bit64_0.9-7                                         beanplot_1.2                                       
 [83] methylumi_2.24.1                                    purrr_0.2.4                                        
 [85] bindrcpp_0.2.2                                      doRNG_1.6.6                                        
 [87] mime_0.5                                            nor1mix_1.2-3                                      
 [89] xml2_1.2.0                                          biomaRt_2.34.2                                     
 [91] compiler_3.4.3                                      rstudioapi_0.7                                     
 [93] beeswarm_0.2.3                                      statmod_1.4.30                                     
 [95] tibble_1.4.2                                        geneplotter_1.56.0                                 
 [97] pcaPP_1.9-73                                        stringi_1.2.2                                      
 [99] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  GenomicFeatures_1.30.3                             
[101] minfi_1.24.0                                        IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[103] lattice_0.20-35                                     Matrix_1.2-14                                      
[105] IlluminaHumanMethylation450kmanifest_0.4.0          multtest_2.34.0                                    
[107] pillar_1.2.2                                        data.table_1.11.2                                  
[109] cowplot_0.9.2                                       bitops_1.0-6                                       
[111] rtracklayer_1.38.3                                  httpuv_1.4.3                                       
[113] R6_2.2.2                                            latticeExtra_0.6-28                                
[115] RMySQL_0.10.15                                      promises_1.0.1                                     
[117] gridExtra_2.3                                       vipor_0.4.5                                        
[119] codetools_0.2-15                                    MASS_7.3-50                                        
[121] assertthat_0.2.0                                    rhdf5_2.22.0                                       
[123] pkgmaker_0.22                                       openssl_1.0.1                                      
[125] GenomicAlignments_1.14.2                            Rsamtools_1.30.0                                   
[127] GenomeInfoDbData_1.0.0                              hms_0.4.2                                          
[129] MultiAssayExperiment_1.4.9                          quadprog_1.5-5                                     
[131] grid_3.4.3                                          rpart_4.1-13                                       
[133] tidyr_0.8.0                                         base64_2.0                                         
[135] illuminaio_0.20.0                                   shiny_1.0.5                                        
[137] base64enc_0.1-3                                     ggbeeswarm_0.6.0 

Sometimes the error message is actually helpful. Running the following:

set.seed(0)
g <- gl(2, 5)
y <- matrix(rnorm(100*length(g)), ncol=length(g))
rownames(y) <- c(NA, 2:nrow(y)) # missing values here!

library(limma)
design <- model.matrix(~g)
fit <- lmFit(y, design)
fit <- eBayes(fit)
topTable(fit, n=Inf)

... yields the error:

Error in data.frame(logFC = M[top]) : row names contain missing values

Hardly surprising, as there are missing values in rownames(y). So get rid of them.