domain/batch-effects
Technical, non-biological variation that confounds measured signal.
18 entries
Molds
- audit-batch-design-validityReferees a batch-aware analysis for validity, returning sourced per-axis verdicts and empirical calibration requirements.
- separate-batch-from-biologySeparates technical variation from biology with explicit design checks, pinned tooling, reproducible adjustment, and a referee handoff.
Papers
- Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
- Tackling the widespread and critical impact of batch effects in high-throughput data
- Asymptotic conditional singular value decomposition for high-dimensional genomic data
- Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
- Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
- OSAT: a tool for sample-to-batch allocations in genomics experiments
- Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results
- ComBat-seq: batch effect adjustment for RNA-seq count data
Tutorials
- DESeq2 vignette — "Analyzing RNA-seq data with DESeq2"
- designit: Blocking and Randomization for Experimental Design
- limma: Linear Models for Microarray and Omics Data — package documentation
- OSAT — "An introduction to OSAT" (Bioconductor vignette + reference manual)
- RNA-seq workflow: gene-level exploratory analysis and differential expression (rnaseqGene)
- The SVA package for removing batch effects and other unwanted variation in high-throughput experiments