```r
countData <- countData[, rownames(colData)]
all(rownames(colData) == colnames(countData)) # This should also return TRUE
```

```
[1] TRUE
```

```r
# Create a DESeqDataSet from count matrix and labels
dds <- DESeqDataSetFromMatrix(countData = countData,
                              colData = colData, design = ~ Condition)


# Run the default analysis for DESeq2 and generate results table
dds <- DESeq(dds)
deseq2.res <- results(dds)

# Sort by adjusted p-value and display
resOrdered <- deseq2.res[order(deseq2.res$padj), ]
vsd <- vst(dds, blind = FALSE)
plotPCA(vsd, intgroup = "Condition")
```

<img src="10.1-hisat-deseq2_files/figure-gfm/unnamed-chunk-26-1.png" style="display: block; margin: auto;" />