I m using this code to make based on EnhancedVolcano plots after using DESeq2. I have 4 groups to compare. Showing 1 comparison identifies 3 significant DE genes.

when I plot the enhanced Volcano plot I find more genes in it. As far as I understand the padjusted value of other genes is NA, they are filtered by DESeq2 packages. I just want to show only those 3 genes which have padj < 0.1. I know I can add their names individually using selectLab, but I have hundreds of genes names to be highlighted?

```{r} dds2 <- DESeq(dds2) resultsNames(dds2)

DE groupPEGEVtreatmentvsPOSFBS

PEGEVtreatmentvsPOSFBS <- results(dds2, cooksCutoff=FALSE, independentFiltering=FALSE, name="groupPEGEVtreatmentvsPOSFBS", alpha = 0.05) #496 summary(PEGEVtreatmentvsPOSFBS) sum(PEGEVtreatmentvsPOSFBS$padj < 0.1, na.rm=TRUE) plotMA(PEGEVtreatmentvsPOSFBS) abline(h = 1, col = "blue") + abline(h = -1, col = "blue")

PEGEVvsPOSFBS <- PEGEVtreatmentvsPOSFBS[which(PEGEVtreatmentvsPOSFBS$pvalue < 0.0001 & abs(PEGEVtreatmentvsPOS_FBS$log2FoldChange) >= 1),]

print("Number of significantally DE genes DE groupPOSFBSvsUCEV:") length(rownames(PEGEVvsPOSFBS)) summary(PEGEVvsPOS_FBS)

PEGEVvsPOSFBS log2 fold change (MLE): group PEG EV treatment vs POS FBS Wald test p-value: group PEG EV treatment vs POS FBS DataFrame with 3 rows and 6 columns baseMean log2FoldChange lfcSE stat <numeric> <numeric> <numeric> <numeric> ABCA1 985.204943402125 1.05865929049936 0.125701824284431 8.42198827682788 C3 742.317002136517 1.96227108910378 0.27988907982447 7.01088835025076 SOD2 2748.61322790313 1.22142861071903 0.0732341596005191 16.6784000442107 pvalue padj <numeric> <numeric> ABCA1 3.70148110922976e-17 1.38805541596116e-13

EnhancedVolcano(PEGEVtreatmentvsPOSFBS, lab = rownames(PEGEVtreatmentvsPOSFBS), x = 'log2FoldChange', y = 'pvalue', xlim = c(-8,8), pCutoff = 0.01, FCcutoff = 1.0, shape = c(6, 6, 19, 16), transcriptPointSize = 1.5, transcriptLabSize = 4.0, title = "Differential expression", subtitle = 'PEGEV versus POSFBS', caption = "FC cutoff, 1; p-value cutoff, 0.0001", legendPosition = "right", legendLabSize = 10, col = c("grey30", "forestgreen", "royalblue", "red2"), colAlpha = 1) ```

Hi, can you confirm what is the problem? - you need to label 100s of genes?; is there enough space to label 100s of genes? Your figure would have to have very large dimensions if you want to label 100s of genes.

I developed EnhancedVolcano; Michael Love developed DESeq2. This question seems to be more about EnhancedVolcano.

You can try selectLab in combination with drawConnectors = TRUE if you want more labels to appear.

Kevin