bioconductor-deseq2

name	bioconductor-deseq2
description	Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
when_to_use	Use when: Two-group comparison (treatment vs control); Multi-factor design with blocking variables; Likelihood ratio test for complex designs; Time-series expression analysis; Allelic imbalance testing
user-invocable	false

DESeq2 — Comprehensive Skill Guide

Domain: RNA-seq Bioconductor: DESeq2 Paper: Love MI, Huber W, Anders S (2014). Genome Biology, 15:550.

Differential gene expression analysis based on the negative binomial distribution. The gold standard for bulk RNA-seq DE analysis.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.52.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: S4Vectors, IRanges, GenomicRanges, SummarizedExperiment
• Imports: BiocGenerics, Biobase, BiocParallel, matrixStats, locfit, ggplot2, Rcpp, MatrixGenerics
• Install: BiocManager::install("DESeq2")

When to Use

• Two-group comparison (treatment vs control)
• Multi-factor design with blocking variables
• Likelihood ratio test for complex designs
• Time-series expression analysis
• Allelic imbalance testing

Alternatives: edgeR, limma-voom, DEXSeq (exon-level)

Do NOT Use When

• Pre-normalised data (TPM, FPKM, RPKM) — use raw integer counts only.
• Single-cell RNA-seq without modifications (use DESeq2 with sfType='poscounts' or use scran/muscat instead).
• N=1 per condition (no replicates) — replicates are mathematically required.
• Continuous response variables — use limma/mixed models instead.
• Proteomics or metabolomics count matrices — distributional assumptions differ.

Data Requirements

Requirement	Details
Min Replicates	≥2 biological replicates per group (≥3 strongly recommended for FDR control)
Input Format	Raw integer count matrix: genes × samples (not normalized values)
Must Not Use	TPM, FPKM, RPKM, or any library-size-normalized values as input
Coverage	≥5–10M uniquely mapped reads per sample recommended; <1M is problematic
Sparsity	Works best with bulk RNA-seq; for highly sparse data (sc) use sfType='poscounts'

Installation

if (!require("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq2")
library(DESeq2)

Workflows

Standard Two-Group Comparison

Comparing treatment vs control with simple design

Import counts

# From count matrix
library(DESeq2)
counts <- read.csv("counts.csv", row.names=1)
coldata <- data.frame(condition=factor(c("ctrl","ctrl","trt","trt")),
                      row.names=colnames(counts))
dds <- DESeqDataSetFromMatrix(countData=counts, colData=coldata,
                               design=~condition)

From tximeta (salmon/alevin counts)

library(tximeta)
se <- tximeta(coldata)          # coldata must have 'names' and 'files' columns
dds <- DESeqDataSet(se, design=~condition)

Pre-filter low-count genes

keep <- rowSums(counts(dds) >= 10) >= 2   # ≥10 counts in ≥2 samples
dds <- dds[keep,]

Run DESeq2

dds <- DESeq(dds)          # estimates: sizeFactors, dispersions, GLM, Wald test
resultsNames(dds)          # show available coefficients

Extract and shrink results

res <- results(dds, contrast=c("condition","trt","ctrl"), alpha=0.05)
res_shrunk <- lfcShrink(dds, coef="condition_trt_vs_ctrl", type="apeglm")
summary(res_shrunk)
sig <- subset(res_shrunk, padj < 0.05 & abs(log2FoldChange) > 1)

Visualise

plotMA(res_shrunk, ylim=c(-5,5))          # MA plot
plotDispEsts(dds)                          # dispersion estimates
vsd <- vst(dds, blind=FALSE)
plotPCA(vsd, intgroup="condition")         # PCA of samples
library(pheatmap)
pheatmap(assay(vsd)[head(order(res$padj),50),])  # top 50 gene heatmap

Multi-factor Design (Batch Correction)

Account for batch/sex/patient while testing condition

Design with nuisance variable

dds <- DESeqDataSetFromMatrix(countData=counts, colData=coldata,
                               design=~batch + condition)
dds <- DESeq(dds)
res <- results(dds, name="condition_treated_vs_untreated")

Visualise after removing batch for plots only

vsd <- vst(dds, blind=FALSE)
# Remove batch effect for visualisation ONLY (never use this as input to DE)
assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$batch)
plotPCA(vsd, intgroup="condition")

Likelihood Ratio Test (LRT) for Complex Designs

Time-series, interaction terms, or any multi-level comparison

LRT comparing full vs reduced model

dds <- DESeqDataSetFromMatrix(counts, coldata, design=~condition+time+condition:time)
dds <- DESeq(dds, test="LRT", reduced=~condition+time)
# Genes significant by LRT show any condition:time interaction
res_lrt <- results(dds)
sig_interaction <- subset(res_lrt, padj < 0.05)

Key Functions & Parameters

DESeqDataSetFromMatrix()

Create DESeqDataSet from count matrix + colData

Parameter	Description
countData	integer matrix of raw counts (genes × samples)
colData	DataFrame of sample metadata
design	R formula specifying model (e.g. ~ condition, ~ batch + condition)

DESeq()

Main wrapper: estimate size factors, dispersions, fit GLM, run Wald/LRT tests

Parameter	Description
object	DESeqDataSet
test	'Wald' (default) or 'LRT'; use LRT for multi-factor / time-series
fitType	'parametric' (default) | 'local' | 'mean' | 'glmGamPoi'
sfType	'ratio' (default) | 'poscounts' | 'iterate'
parallel	logical; use BiocParallel for large datasets

results()

Extract results table with log2FC, p-value, padj

Parameter	Description
object	DESeqDataSet
contrast	vector c('factor','numerator','denominator') or numeric for LRT
alpha	significance threshold for independent filtering (default 0.1)
lfcThreshold	test against this minimum |log2FC| (default 0); use with altHypothesis
altHypothesis	'greaterAbs'|'lessAbs'|'greater'|'less'
independentFiltering	logical; filter low-mean genes (default TRUE)
cooksCutoff	flag outliers above Cook's distance threshold

lfcShrink()

Shrink log2 fold-change estimates (STRONGLY RECOMMENDED for ranking/visualisation)

Parameter	Description
dds	DESeqDataSet after DESeq()
coef	coefficient name or index (use resultsNames(dds) to see options)
type	'apeglm' (default, best) | 'ashr' | 'normal'
res	optional: supply existing results() object

vst()

Variance Stabilising Transformation for visualisation/clustering (fast)

Parameter	Description
object	DESeqDataSet
blind	TRUE (unsupervised, default) or FALSE (use design)
nsub	number of genes used to estimate dispersion (default 1000)

rlog()

Regularised log2 transformation; better for small n, slower than vst

Parameter	Description
object	DESeqDataSet
blind	TRUE (default) or FALSE

Scientific Assumptions

The method assumes the following about your data and experiment:

• Counts follow a negative binomial (NB) distribution.
• The dispersion parameter (φ) is estimated from data and shrunk toward a common trend.
• Genes are not differentially expressed between most samples (used to estimate size factors).
• Library sizes (or size factors) capture the main technical variation.
• Within-group expression is approximately exchangeable (biological replication).

Result Interpretation

• log2FoldChange (raw): can be noisy for low-count genes — always report the SHRUNKEN LFC from lfcShrink().
• padj (BH-adjusted p-value): 0.05 → 5% expected false discoveries among all genes you call significant.
• pvalue (raw): report padj in papers, not raw p-value.
• baseMean: average normalized count across ALL samples; low baseMean (< 5) → high uncertainty, treat cautiously.
• NA in padj: gene was filtered by independent filtering (too low count) or Cook's outlier — not a bug.
• Volcano plot: plot log2FoldChange (shrunken) vs -log10(padj). Use padj<0.05 & |LFC|>1 as typical cutoff.
• MA plot (plotMA): expected to show points symmetrically around 0; systematic bias indicates normalization issue.

Best Practices

• Always use raw counts, never pre-normalised values (RPKM/TPM).
• Pre-filter genes with very low counts: keep <- rowSums(counts(dds) >= 10) >= 3
• Use lfcShrink(type='apeglm') for final LFC estimates and volcano/MA plots.
• For designs with a nuisance variable (batch), put it in design as ~ batch + condition.
• Use test='LRT' when comparing a complex model vs reduced model (time-series, interaction).
• Check size factors: very large or small values (>5 or <0.2) indicate composition bias.
• Check Cook's distance outlier genes; set cooksCutoff=FALSE to disable flagging.
• For single-cell / very sparse data consider sfType='poscounts'.
• Use plotDispEsts(dds) to verify dispersion estimates before trusting results.
• Use DESeqDataSetFromTximeta() instead of matrix import when using salmon/alevin counts.

When to Choose This vs Alternatives

Alternative	Prefer this tool when	Prefer alternative when
edgeR	You have ≥3 replicates per group; you want apeglm LFC shrinkage; you prefer Bayesian-style shrinkage approach.	You have very small n (2 per group); you need quasi-likelihood F-tests; you prefer exact negative binomial tests.
limma-voom	You are working with count data from a well-powered experiment (≥5 replicates).	You have microarray data, large n (≥10/group), or want to use linear model contrasts flexibly.
fishpond (Swish)	Your data comes from Salmon and you have bootstrap replicates; you want robust transcript-level DE.	You want gene-level DE from any aligner (STAR+featureCounts etc.) without bootstraps.

Benchmark Evidence

Key studies that have validated or benchmarked this tool:

• Love MI, Huber W, Anders S (2014). Genome Biol 15:550. PMID:25516281
  Original DESeq2 paper demonstrating superior FDR control and power vs simple fold-change ranking.

• Rapaport F et al. (2013). Genome Biol 14:R95. PMID:24651052
  Benchmark: DESeq2 and edgeR outperform other methods in sensitivity/specificity; DESeq2 better FDR control at low counts.

• Love MI et al. (2015). F1000Research 4:1070. PMID:29481549
  End-to-end RNA-seq workflow paper demonstrating DESeq2 from Salmon → tximeta → DE analysis.

Common Errors & Troubleshooting

Error in checkForExperimentalReplicates: ...

Cause: Only one sample per condition — DESeq2 needs replicates

Fix: You must have ≥2 biological replicates per group

Error: every gene contains at least one zero

Cause: Using VST/rlog on a dataset with all-zero genes

Fix: Pre-filter: dds <- dds[rowSums(counts(dds)) > 0,]

NA p-values for some genes

Cause: Genes with all-zero counts OR extreme Cook's distance outliers

Fix: Expected — these are filtered by independent filtering / Cook's cutoff

model matrix not full rank

Cause: Perfect collinearity in the design matrix (e.g. batch confounds condition)

Fix: Drop one level or use a different design; run colnames(model.matrix(~cond,df))

From Community Q&A (Biostars)

• DiffBind normalization error: invalid argument type (list) - cannot make it work everything seems co
• DESeq2: error in checkFullRank(modelMatrix)
• Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR DESeq2 a
• Contrasts for comparing condition within tissue
• PyDeseq2 - InvalidIndexError

Additional Notes from Official Documentation

Extracted from the DESeq2 Bioconductor vignette(s)

11/13/2025

A basic task in the analysis of count data from RNA-seq is the detection of differentially expressed genes. The count data are presented as a table which reports, for each sample, the number of sequence fragments that have been assigned to each gene. Analogous data also arise for other assay types, including comparative ChIP-Seq, HiC, shRNA screening, and mass spectrometry. An important analysis question is the quantification and statistical inference of systematic changes between conditions, as compared to within-condition variability. The package DESeq2 provides methods to test for differential expression by use of negative binomial generalized linear models; the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions. This vignette explains the

Standard workflow

Note: if you use DESeq2 in published research, please cite: Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology , 15 :550. 10.1186/s13059-014-0550-8 Other Bioconductor packages with similar aims are edgeR , limma , DSS , EBSeq , and baySeq .

Quick start

Here we show the most basic steps for a differential expression analysis. There are a variety of steps upstream of DESeq2 that result in the generation of counts or estimated counts for each sample, which we will discuss in the sections below. This code chunk assumes that you have a count matrix called cts and a table of sample information called coldata . The design indicates how to model the samples, here, that we want to measure the effect of the condition, controlling for batch differences. The two factor variables batch and condition should be columns of coldata . The following starting functions will be explained below: If you have performed transcript quantification (with Salmon , kallisto , RSEM , etc.) you could import the data with tximport , which produces a list, and then you

dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design= ~ batch + condition)
dds <- DESeq(dds)
resultsNames(dds) # lists the coefficients
res <- results(dds, name="condition_trt_vs_untrt")
# or to shrink log fold changes association with condition:
res <- lfcShrink(dds, coef="condition_trt_vs_untrt", type="apeglm")

How to get help for DESeq2

Any and all DESeq2 questions should be posted to the Bioconductor support site , which serves as a searchable knowledge base of questions and answers: https://support.bioconductor.org Posting a question and tagging with “DESeq2” will automatically send an alert to the package authors to respond on the support site. See the first question in the list of Frequently Asked Questions (FAQ) for information about how to construct an informative post. You should not email your question to the package authors, as we will just reply that the question should be posted to the Bioconductor support site .

Acknowledgments

We have benefited in the development of DESeq2 from the help and feedback of many individuals, including but not limited to: The Bionconductor Core Team, Alejandro Reyes, Andrzej Oles, Aleksandra Pekowska, Felix Klein (early testers), Constantin Ahlmann-Eltze (glmGamPoi), Nikolaos Ignatiadis (IHW, greaterAbs), Raphael Rossellini (greaterAbs), Anqi Zhu (apeglm), Joseph Ibrahim (apeglm), Vince Carey, Owen Solberg, Ruping Sun, Devon Ryan, Steve Lianoglou, Jessica Larson, Christina Chaivorapol, Pan Du, Richard Bourgon, Willem Talloen, Elin Videvall, Hanneke van Deutekom, Todd Burwell, Jesse Rowley, Igor Dolgalev, Stephen Turner, Ryan C Thompson, Tyr Wiesner-Hanks, Konrad Rudolph, David Robinson, Mingxiang Teng, Mathias Lesche, Sonali Arora, Jordan Ramilowski, Ian Dworkin, Bjorn Gruning, Ryan

Funding

DESeq2 and its developers have been partially supported by funding from the European Union’s 7th Framework Programme via Project RADIANT, NIH NHGRI R01-HG009937, and by a CZI EOSS award. ELIXIR feedback: Your feedback matters! Please take our quick user satisfaction survey: link

Why un-normalized counts?

As input, the DESeq2 package expects count data as obtained, e.g., from RNA-seq or another high-throughput sequencing experiment, in the form of a matrix of integer values. The value in the i -th row and the j -th column of the matrix tells how many reads can be assigned to gene i in sample j . Analogously, for other types of assays, the rows of the matrix might correspond e.g. to binding regions (with ChIP-Seq) or peptide sequences (with quantitative mass spectrometry). We will list method for obtaining count matrices in sections below. The values in the matrix should be un-normalized counts or estimated counts of sequencing reads (for single-end RNA-seq) or fragments (for paired-end RNA-seq). The RNA-seq workflow describes multiple techniques for preparing such count matrices. It is im

The DESeqDataSet

The object class used by the DESeq2 package to store the read counts and the intermediate estimated quantities during statistical analysis is the DESeqDataSet , which will usually be represented in the code here as an object dds . A technical detail is that the DESeqDataSet class extends the RangedSummarizedExperiment class of the SummarizedExperiment package. The “Ranged” part refers to the fact that the rows of the assay data (here, the counts) can be associated with genomic ranges (the exons of genes). This association facilitates downstream exploration of results, making use of other Bioconductor packages’ range-based functionality (e.g. find the closest ChIP-seq peaks to the differentially expressed genes). A DESeqDataSet object must have an associated design formula . The des

Resources

• Bioconductor page: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
• GitHub: https://github.com/mikelove/DESeq2
• Bioconductor support forum: https://support.bioconductor.org/
• Paper: Love MI, Huber W, Anders S (2014). Genome Biology, 15:550.

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