I have used limma voom for a simple RNAseq experiment (with two conditions), and in the end many genes have exactly the same adjusted p-value. I was wondering if this is an artifact? Or an error in the program? Or any other explanation?
In a nutshell here the essential code.
dge <- DGEList(counts=counts) keep <- rowSums(cpm(dge)>1) >= 3 dge2 <- dge[keep,] y1 <- calcNormFactors(dge2) dim(y1) # 13597 v <- voom(y1, design, plot=TRUE) fit <- lmFit(v, design) contr <- makeContrasts( TreatsControl = Treat-Control, levels = design) fit2 <- eBayes(contrasts.fit(fit, contr)) topTable(fit2) logFC AveExpr t P.Value adj.P.Val B ENSG00000x 1.2876594 5.909082 16.08384 2.420048e-06 0.008157177 5.642434 ENSG00000x 1.6732008 4.513546 16.50495 2.064063e-06 0.008157177 5.629066 ENSG00000x 1.6447710 4.407068 14.42668 4.717211e-06 0.008157177 4.903185 ENSG00000x 0.8961535 9.105814 13.99453 5.681749e-06 0.008157177 4.866960 ENSG00000x 1.8755434 8.735065 13.73668 6.365353e-06 0.008157177 4.755742 ENSG00000x 1.0970506 8.481634 13.47671 7.152532e-06 0.008157177 4.641336 ENSG00000x 2.0074732 2.637772 15.16813 3.469509e-06 0.008157177 4.612408 ENSG00000x 1.0538233 4.869446 13.48162 7.136669e-06 0.008157177 4.601666 ENSG00000x 1.6564010 5.035228 13.41057 7.370392e-06 0.008157177 4.576627 ENSG00000x 0.8405514 6.563975 13.07226 8.611902e-06 0.008157177 4.457263
As you can see, the adjusted p-values are exactly the same, while the normal p-values differ. Any ideas about the cause? Has anyone seen this before?
> sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] 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_3.20.5 limma_3.34.5 loaded via a namespace (and not attached): [1] compiler_3.4.3 Rcpp_0.12.14 grid_3.4.3 locfit_1.5-9.1 [5] lattice_0.20-35
Perry, thanks for explanation and link to earlier posts!