Gene-level QC and differential expression (DESeq2)

Last updated on 2025-11-25 | Edit this page

Overview

Questions

  • How do we explore RNA seq count data before running DESeq2.
  • How do we restrict analysis to protein coding genes.
  • How do we perform differential expression with DESeq2.
  • How do we visualize sample relationships and DE genes.
  • How do we save a useful DE results table with annotation and expression values.

Objectives

  • Import count and sample metadata into R.
  • Attach biotype and gene symbol annotation to Ensembl gene IDs.
  • Explore library sizes, variance stabilizing transforms, distances, and PCA.
  • Run DESeq2 for a two group comparison.
  • Create a volcano plot with gene symbols.
  • Export joined DE results including normalized counts and annotation.

Introduction

In this episode we move from count matrices to differential expression analysis and visualization.

The workflow has four parts:

  1. Import counts and sample metadata.
  2. Exploratory analysis on protein coding genes (quality checks).
  3. Differential expression analysis with DESeq2.
  4. Visualization and export of annotated DE results.
Prerequisite

What you need for this episode

  • gene_counts_clean.txt generated from featureCounts
  • a samples.csv file describing the experimental groups
  • RStudio session on Scholar using Open OnDemand

While we created the count matrix in the previous episode, we still need to create a sample metadata file. This file should contain at least two columns: sample names matching the count matrix column names, and the experimental condition (e.g., control vs treatment). Simply copy/paste the following into a text file and save it in your scripts directory as samples.csv:

sample,condition
SRR33253285,Nat10-CKO
SRR33253286,Nat10-CKO
SRR33253287,Nat10-CKO
SRR33253288,Nat10floxflox
SRR33253289,Nat10flox/flox
SRR33253290,Nat10flox/flox

Also, create a direcotry for DESeq2 results:

BASH 

mkdir -p results/deseq2

All analyses are performed in R through Open OnDemand

Step 1: Start Open OnDemand R session and prepare data

We will be using the OOD to start an interactive session on Scholar: https://gateway.negishi.rcac.purdue.edu

  1. Login using your Purdue credentials after clicking the above link
  2. Click on “Interactive Apps” in the top menu, and select “RStudio (Bioconductor)”
  3. Fill the job submission form as follows:
    • queue: workshop
    • Walltime: 4
    • Number of cores: 4
  4. Click “Launch” and wait for the RStudio session to start
  5. Once the session starts, you’ll will be able to click on “Connect to RStudio server” which will open the RStudio interface.
Open OnDemand interface
Open OnDemand interface

Once in RStudio, load the necessary libraries:

Setup: load packages and data

R 

library(RColorBrewer)
library(EnsDb.Mmusculus.v79)
library(ensembldb)
library(tidyverse)
library(DESeq2)
library(ggplot2)
library(pheatmap)
library(readr)
library(dplyr)
library(ComplexHeatmap)
library(ggrepel)
library(vsn)
# Modify the path as needed
setwd("/scratch/negishi/aseethar/rnaseq-workshop")

countsFile <- "results/counts/gene_counts_clean.txt"
# prepare this file first!
groupFile  <- "scripts/samples.csv"

coldata <-
  read.csv(
    groupFile,
    row.names = 1,
    header = TRUE,
    stringsAsFactors = TRUE
  )
coldata$condition <- as.factor(coldata$condition)

cts <- as.matrix(read.delim(countsFile, row.names = 1, header = TRUE))

We also load gene level annotation tables prepared earlier.

R 

mart <-
  read.csv(
    "data/mart.tsv",
    sep = "\t",
    header = TRUE
  )

annot <-
  read.csv(
    "data/annot.tsv",
    sep = "\t",
    header = TRUE
  )

Since the gene IDs in the count matrix are Ensembl IDs, it will be hard to interpret the results without annotation. We will need to use the org.Mm.eg.db package for attaching gene symbols, so we can interpret the results better.0

R 

library(biomaRt)
library(tidyverse)
# select Mart
ensembl = useMart("ENSEMBL_MART_ENSEMBL")
# we need to use the correct dataset for mouse
# we will query the available datasets and filter for mouse (GRCm39)
listDatasets(ensembl) %>%
  filter(str_detect(description, "GRCm39"))
# we can use the dataset name to set the dataset
ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)
# our counts have Ensembl gene IDs with version numbers
# lets find how it is referred in biomaRt
listFilters(ensembl) %>%
  filter(str_detect(name, "ensembl"))
# so we will now set the filter type accordingly
filterType <- "ensembl_gene_id_version"
# from our counts data, get the list of gene IDs
filterValues <- rownames(counts)
# take a look at the available attributes (first 20)
listAttributes(ensembl) %>%
     head(20)
# we will retrieve ensembl gene id, ensembl gene id with version and external gene name
attributeNames <- c('ensembl_gene_id',
                    'ensembl_gene_id_version',
                    'external_gene_name',
                    'gene_biotype',
                    'description')
# get the annotation
annot <- getBM(
  attributes = attributeNames,
  filters = filterType,
  values = filterValues,
  mart = ensembl
)
saveRDS(annot, file = "results/counts/gene_annotation.rds")
# also save as tsv for future use
write.table(
  annot,
  file = "data/mart.tsv",
  sep = "\t",
  quote = FALSE,
  row.names = FALSE
)
# save a simplified annotation file with only essential columns
mart %>% 
select(ensembl_gene_id, ensembl_gene_id_version, external_gene_name) %>%
  write.table(
    file = "data/annot.tsv",
    sep = "\t",
    quote = FALSE,
    row.names = FALSE

The objects loaded here form the foundation for the entire workflow. cts contains raw gene counts from featureCounts. coldata contains the metadata that describes each sample and defines the comparison groups. mart and annot contain functional information for each gene so we can attach gene symbols and biotypes later in the analysis.

Callout

Sample metadata and design

coldata must have row names that match the count matrix column names. The condition column defines the groups for DESeq2 (Nat10-CKO vs Nat10flox/flox).

Exploratory analysis

Attach annotation and filter to protein coding genes

We first join counts with biotype information from mart and filter to protein coding genes.

R 

cts_tbl <- cts %>%
  as.data.frame() %>%
  rownames_to_column("ensembl_gene_id_version")

cts_annot <- cts_tbl %>%
  left_join(mart, by = "ensembl_gene_id_version")

sum(is.na(cts_annot$gene_biotype))

Joining annotation allows us to move beyond raw Ensembl IDs. This step attaches gene symbols, biotypes, and descriptions so that later plots and tables are interpretable. At this point the dataset is still large and includes many noncoding genes, pseudogenes, and biotypes we won’t analyze further.

Summarize gene biotypes:

R 

biotype_df <- cts_annot %>%
  dplyr::count(gene_biotype, name = "n") %>%
  arrange(desc(n))

ggplot(biotype_df, aes(x = reorder(gene_biotype, n), y = n)) +
  geom_col(fill = "steelblue") +
  coord_flip() +
  theme_minimal() +
  labs(
    x = "Gene biotype",
    y = "Number of genes",
    title = "Distribution of gene biotypes in annotation"
  )
Distribution of gene biotypes in annotation
Distribution of gene biotypes in annotation

Visualizing biotype composition gives a sense of how many genes belong to each functional class. RNA-seq quantifies all transcribed loci, but many biotypes (snRNA, TEC, pseudogenes) are not suitable for differential expression with DESeq2 because they tend to be lowly expressed or unstable. This motivates filtering to protein-coding genes for QC and visualization.

Filter to protein coding genes and lowly expressed genes:

R 


cts_coding <- cts_annot %>%
    filter(gene_biotype == "protein_coding") %>%
    filter(rowSums(across(all_of(rownames(coldata)))) > 5) %>%
    select(ensembl_gene_id_version, all_of(rownames(coldata))) %>%
    column_to_rownames("ensembl_gene_id_version")

dim(cts_coding)
[1] 15839     6
Callout

Why filter protein coding genes and low expression

Noncoding biotypes (lncRNA, pseudogene, etc.) can be biologically important. Filtering lowly expressed genes reduces noise in exploratory analyses. Genes with near-zero counts across all samples inflate variance estimates and obscure real biological structure. The threshold of 5 total counts is a conservative filter that keeps genes with minimal but genuine expression while removing background noise.

Library size differences

We summarize total counts per sample for protein coding genes.

R 

libSize <- colSums(cts_coding) %>%
  as.data.frame() %>%
  rownames_to_column("sample") %>%
  rename(total_counts = 2) %>%
  mutate(total_millions = total_counts / 1e6)

ggplot(libSize, aes(x = sample, y = total_counts)) +
  geom_col(fill = "steelblue") +
  theme_minimal() +
  labs(
    x = "Sample",
    y = "Total assigned reads",
    title = "Total reads per sample"
  ) +
  theme(
    axis.text.x = element_text(angle = 45, hjust = 1)
  )
Total assigned reads per sample
Total assigned reads per sample

Library size differences affect normalization. Although DESeq2 corrects for this through size factors, inspecting raw library sizes ensures no sample has abnormally low sequencing depth, which could compromise downstream analyses.

Create DESeq2 object for exploratory plots

R 

dds <- DESeqDataSetFromMatrix(
  countData = cts_coding,
  colData   = coldata,
  design    = ~ condition
)

dds <- estimateSizeFactors(dds)

Inspect size factors vs library size:

R 

ggplot(
  data.frame(
    libSize    = colSums(assay(dds)),
    sizeFactor = sizeFactors(dds),
    Group      = dds$condition
  ),
  aes(x = libSize, y = sizeFactor, col = Group)
) +
  geom_point(size = 5) +
  theme_bw() +
  labs(x = "Library size", y = "Size factor")
Size factors vs library size
Size factors vs library size

Variance stabilization and mean SD plots

Raw count data have a strong mean–variance dependency: low count genes have high variance, and high count genes show lower relative variability. This makes Euclidean distance and PCA misleading on raw counts. VST removes this dependency so that downstream clustering is biologically meaningful rather than driven by count scale.

Inspect mean vs standard deviation plot before transformation:

R 

meanSdPlot(assay(dds), ranks = FALSE)
average counts vs variance
average counts vs variance

Apply variance stabilizing transform (VST):

R 

vsd <- DESeq2::vst(dds, blind = TRUE)
meanSdPlot(assay(vsd), ranks = FALSE)
average counts vs variance after transformation
average counts vs variance after transformation
Callout

Why use VST

Counts have mean dependent variance. Variance stabilizing transform (VST) makes the variance roughly constant across the range, which improves distance based methods and PCA.

Sample to sample distances

The distance heatmap helps answer a key question: Do samples group by biological condition or by an unwanted variable (batch, sequencing run, contamination)? This is one of the fastest ways to detect outliers.

R 

sampleDists       <- dist(t(assay(vsd)))
sampleDistMatrix  <- as.matrix(sampleDists)
rownames(sampleDistMatrix) <- colnames(vsd)
colnames(sampleDistMatrix) <- NULL
colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)

pheatmap(
  sampleDistMatrix,
  clustering_distance_rows = sampleDists,
  clustering_distance_cols = sampleDists,
  col                      = colors
)
Eucledean distance heatmap
Eucledean distance heatmap

PCA on top variable genes

PCA projects samples into low-dimensional space and reveals dominant sources of variation. Ideally, samples separate by biological condition along one of the top PCs. If not, the signal from the condition may be weak or confounded by other factors.

R 

rv <- rowVars(assay(vsd))
select <- order(rv, decreasing = TRUE)[seq_len(min(500, length(rv)))]

pca <- prcomp(t(assay(vsd)[select, ]))
percentVar <- pca$sdev ^ 2 / sum(pca$sdev ^ 2)

intgroup    <- "condition"
intgroup.df <- as.data.frame(colData(vsd)[, intgroup, drop = FALSE])

group <- if (length(intgroup) == 1) {
  factor(apply(intgroup.df, 1, paste, collapse = " : "))
}

d <- data.frame(
  PC1 = pca$x[, 1],
  PC2 = pca$x[, 2],
  intgroup.df,
  name = colnames(vsd)
)

ggplot(d, aes(PC1, PC2, color = condition)) +
  scale_shape_manual(values = 1:12) +
  scale_color_manual(values = c(
    "Nat10-CKO"       = "#00b462",
    "Nat10flox/flox"  = "#980c80"
  )) +
  theme_bw() +
  theme(legend.title = element_blank()) +
  geom_point(size = 2, stroke = 2) +
  geom_text_repel(aes(label = name)) +
  xlab(paste("PC1", round(percentVar[1] * 100, 2), "% variance")) +
  ylab(paste("PC2", round(percentVar[2] * 100, 2), "% variance"))
PCA plot showing sample clustering
PCA plot showing sample clustering
Challenge

Exercise: interpret exploratory plots

Using the library size, distance heatmap, and PCA:

  1. Are there any obvious outlier samples.
  2. Do replicates from the same condition cluster together.
  3. Does any sample look inconsistent with its metadata label.

Example interpretation:

  1. Library sizes are comparable across samples and fall within a narrow range.
  2. Samples cluster by condition in both distance heatmaps and PCA.
  3. No sample appears as a clear outlier relative to its group.

Differential gene expression analysis

For DE testing we use the full count matrix (cts) without filtering by biotype. This preserves all features counted by featureCounts.

R 

dds <- DESeqDataSetFromMatrix(
  countData = cts_coding,
  colData   = coldata,
  design    = ~ condition
)

You can either run the individual DESeq2 steps:

R 

dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomWaldTest(dds)

Above three steps can be run together using the DESeq function:

R 

dds <- DESeq(dds)
estimating size factors
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not a warning or an error]
final dispersion estimates
fitting model and testing

Inspect dispersion estimates:

R 

plotDispEsts(dds)
Dispersion estimates from DESeq2
Dispersion estimates from DESeq2

Obtain results for the contrast of interest (Nat10flox/flox vs Nat10-CKO):

R 

res <-
  results(
    dds,
    contrast = c(
      "condition",
      "Nat10flox/flox",
      "Nat10-CKO"
    )
  )

summary(res)

TXT 

out of 15839 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)       : 3195, 20%
LFC < 0 (down)     : 3398, 21%
outliers [1]       : 362, 2.3%
low counts [2]     : 308, 1.9%
(mean count < 1)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

Order the results by p value to see the top DE genes:

R 

head(res[order(res$pvalue), ])
log2 fold change (MLE): condition Nat10flox/flox vs Nat10-CKO
Wald test p-value: condition Nat10flox.flox vs Nat10.CKO
DataFrame with 6 rows and 6 columns
       baseMean log2FoldChange     lfcSE      stat       pvalue         padj
      <numeric>      <numeric> <numeric> <numeric>    <numeric>    <numeric>
18512   4645.33       -5.17453 0.1335387  -38.7493  0.00000e+00  0.00000e+00
940     5041.68       -2.88015 0.1039939  -27.6953 7.94364e-169 6.02485e-165
13789  14362.27       -2.40229 0.0951377  -25.2506 1.11514e-140 5.63852e-137
16183  42766.77       -4.68585 0.1923780  -24.3575 4.82857e-131 1.83111e-127
18278   7055.06       -3.48409 0.1535305  -22.6932 5.23170e-114 1.58719e-110
270     1469.83       -2.87951 0.1298316  -22.1788 5.50606e-109 1.39202e-105

Each row represents one gene. Key columns: baseMean: average normalized count across all samples log2FoldChange: direction and magnitude of change between groups pvalue / padj: statistical significance after multiple testing correction Genes with NA values often have too few reads to estimate dispersion and should not be interpreted.

Create a summary table:

R 

log2fc_cut <- log2(1.5)

res_df <- as.data.frame(res)

summary_table <- tibble(
    total_genes = nrow(res_df),
    sig = sum(res_df$padj < 0.05, na.rm = TRUE),
    up  = sum(res_df$padj < 0.05 & res_df$log2FoldChange >  log2fc_cut, na.rm = TRUE),
    down= sum(res_df$padj < 0.05 & res_df$log2FoldChange < -log2fc_cut, na.rm = TRUE)
)
print(summary_table)
# A tibble: 1 × 4
  total_genes   sig    up  down
        <int> <int> <int> <int>
1       15839  5658  2180  2363

Keep gene IDs:

R 

res_df <- as.data.frame(res)
res_df$ensembl_gene_id_version <- rownames(res_df)

Joining results with expression and annotation

Get normalized counts:

R 

norm_counts    <- counts(dds, normalized = TRUE)
norm_counts_df <- as.data.frame(norm_counts)
norm_counts_df$ensembl_gene_id_version <- rownames(norm_counts_df)

Join DE results, normalized counts, and annotation:

R 

res_annot <- res_df %>%
  dplyr::left_join(norm_counts_df,
                   by = "ensembl_gene_id_version") %>%
  dplyr::left_join(mart,
                   by = "ensembl_gene_id_version")

Joining normalized counts and annotation makes the output biologically interpretable. The final table becomes a comprehensive results object containing: - gene identifiers - gene symbols - functional descriptions - differential expression statistics - normalized expression values This is the format most researchers expect when examining results or importing them into downstream tools.

Define significance labels for plotting:

R 

log2fc_cut <- log2(1.5)

res_annot <- res_annot %>%
  dplyr::mutate(
    label = dplyr::coalesce(external_gene_name, ensembl_gene_id_version),
    sig = dplyr::case_when(
      padj <= 0.05 & log2FoldChange >=  log2fc_cut ~ "up",
      padj <= 0.05 & log2FoldChange <= -log2fc_cut ~ "down",
      TRUE ~ "ns"
    )
  )

Visualization: volcano plot

The volcano plot summarizes statistical significance (padj) and effect size (log2FoldChange) simultaneously. Genes far left or right show strong expression differences. Genes high on the plot pass stringent significance thresholds. Labels help identify the most biologically meaningful genes.

R 

ggplot(
  res_annot,
  aes(
    x     = log2FoldChange,
    y     = -log10(padj),
    col   = sig,
    label = label
  )
) +
  geom_point(alpha = 0.6) +
  scale_color_manual(values = c(
    "up"   = "firebrick",
    "down" = "dodgerblue3",
    "ns"   = "grey70"
  )) +
  geom_text_repel(
    data = dplyr::filter(res_annot, sig != "ns"),
    max.overlaps       = 12,
    min.segment.length = Inf,
    box.padding        = 0.3,
    seed               = 42,
    show.legend        = FALSE
  ) +
  theme_classic() +
  xlab("log2 fold change") +
  ylab("-log10 adjusted p value") +
  ggtitle("Volcano plot: Nat10-CKO vs Nat10flox/flox")
Volcano plot of differential expression results
Volcano plot of differential expression results
Callout

Interpreting the volcano

Points to the right are higher in Nat10flox/flox, to the left are higher in Nat10-CKO. Points near the top have stronger statistical support (small adjusted p values). Colored points mark genes that pass both fold change and padj thresholds.

Saving results

Saving both the full table and the significant subset allows flexibility: - The full table is needed for pathway analyses and reproducibility. - The subset table focuses on interpretable and biologically meaningful DE genes.

R 

readr::write_tsv(
  res_annot,
  "results/deseq2/DESeq2_results_joined.tsv"
)

Filter to significant genes (padj ≤ 0.05 and fold change ≥ 1.5):

R 

sig_res <- res_annot %>%
  dplyr::filter(
    padj <= 0.05,
    abs(log2FoldChange) >= log2fc_cut
  )

readr::write_tsv(
  sig_res,
  "results/deseq2/DESeq2_results_sig.tsv"
)
Challenge

Exercise: explore top DE genes

Using sig_res:

  1. Which genes have the largest positive log2 fold change.
  2. Which genes have the largest negative log2 fold change.
  3. Are any of the top genes known to be related to Nat10 function or the studied phenotype.

Example interpretation:

  • Several strongly up regulated genes are involved in cell cycle and RNA processing.
  • Strongly down regulated genes may include transcription factors and signaling components.
  • Cross referencing top hits with prior literature or databases can reveal mechanistic hypotheses.

Summary

Key Points
  • Counts and sample metadata must be aligned before building DESeq2 objects.
  • Biotype annotation allows restriction to protein coding genes for exploratory QC.
  • Variance stabilizing transform, distance heatmaps, and PCA help detect outliers and batch effects.
  • DESeq2 provides a complete pipeline from raw counts to differential expression.
  • Joining DE results with normalized counts and gene annotation yields a useful final table.
  • Volcano plots summarize differential expression using fold change and adjusted p values.