after updating R and edgeR I lost the annotations in the final Diff.Expressed matrix (toptags) when running the edgeR pipeline. How do I get the row.names from the data matrix into the topTag-matrix? data <- read.table("KO_and_WT_Summary_miRNA_Expression.csv", row.names=1, sep="", header=T) head(data) T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h C0h C0.25h mmu-let-7a-1-3p 450 329 395 300 469 320 245 281 300 376 166 242 mmu-let-7a-5p 93070 62871 65013 69714 73983 60836 49885 63788 62161 65595 48525 32111 mmu-let-7c-2-3p 436 325 391 295 466 314 243 278 300 376 152 220 mmu-let-7c-5p 544 367 350 492 331 266 323 309 403 613 255 219 mmu-let-7d-3p 7397 5854 5280 6883 5021 5117 5327 6137 5649 5197 6460 3951 mmu-let-7d-5p 8893 7584 7082 8062 6258 6423 6120 7053 7000 6998 7265 3712 keep <- rowSums(cpm(data)>2) >=2 data <- data[keep, ] table(keep) y <- DGEList(counts=data[,1:18], genes=data[,0:1]) y <- calcNormFactors(y) y$samples plotMDS(y,main="") Time=c("0.25h","0.5h","1h","2h","3h","6h","12h","24h","48h","0.25h","0 .5h","1h","2h","3h","6h","12h","24h","48h") Condition=c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT","WT","WT ","WT","WT","WT","WT","WT","WT") design <- model.matrix(~0+Time+Condition) rownames(design) <- colnames(y) y <- estimateGLMCommonDisp(y, design, verbose=TRUE, method="deviance",robust=TRUE, subset=NULL) y <- estimateGLMTrendedDisp(y, design) y <- estimateGLMTagwiseDisp(y, design) fit <- glmFit(y, design) lrt <- glmLRT(fit) topTags(lrt) Coefficient: ConditionWT genes logFC logCPM LR PValue FDR 189 5128 -11.028422 7.905804 4456.297 0 0 188 12271 -10.582267 9.061326 5232.075 0 0 167 121120 -9.831894 12.475576 5957.104 0 0 34 255235 -9.771266 13.592968 7355.592 0 0 168 311906 -9.597952 13.907951 10710.111 0 0 166 631262 -9.592550 14.932018 11719.222 0 0 79 79 9.517226 11.466696 7964.269 0 0 169 2512 -8.946429 6.758584 2502.548 0 0 448 3711 -7.650068 7.764682 2914.784 0 0 32 260769 -7.412197 13.633352 4906.198 0 0 -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] reshape2_1.2.2 ggplot2_0.9.3.1 edgeR_3.2.4 limma_3.16.7 loaded via a namespace (and not attached): [1] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 grid_3.0.1 [5] gtable_0.1.2 labeling_0.2 MASS_7.3-26 munsell_0.4.2 [9] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 scales_0.2.3 [13] stringr_0.6.2 tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.