Hello. I am working with RNA seq data, and I am trying to do differential expression analysis. I am trying to make a PCA plot with Deseq2. Howevere although I have 12 samples, the PCA plot appears to have 11 dots. When I am making MDS plot with limma voom I see the same (11 dots instead of 12). I have checked dds object (and rlog transformed respectively) and its dimensions is 12. What could be the cause? Thank you!
dds <- DESeqDataSetFromMatrix(countData=countData, colData=colData, design=~group) keep <- rowSums(counts(dds)) >= 10 dds <- dds[keep,] rld <- rlog(dds) plot_pca<-plotPCA(rld, intgroup = c("group")) plotPCA(rld, intgroup = c("group")) plot_pca <- plot_pca + geom_text(aes_string(label = "name"), color = "black") print(plot_pca)