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2 hours ago by

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)

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modified 2 hours ago

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2 hours ago
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eridanus0



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