ArticleNucleic acids research2019
A new normalization for Nanostring nCounter gene expression data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Medicinal cannabis plant extract (NTI164) modifies epigenetic, ribosomal, and immune pathways in paediatric acute-onset neuropsychiatric syndrome.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Trial
- Normalization of nCounter Gene Expression Data Alters Molecular Diagnostics in Kidney Transplantation.Journal of the American Society of Nephrology : JASN · 2026Article
- BOLD-100 in Combination with FOLFOX Is a Broadly Effective Therapeutic Strategy for Gastric Cancer.International journal of molecular sciences · 2026Article
- Inflammation-Associated Transcriptional Remodeling of Antioxidant and Stress Signaling Pathways in First-Trimester Placenta in Maternal Overweight and Obesity.Biomolecules · 2026Article
- Tumor-resident T cells and dendritic cells form an in situ archetype during immunotherapy response in melanoma.Nature communications · 2026Article
- Pyroxd1 is essential for murine viability with the homozygous N155S recurrent variant linked to myopathy, muscle hypotrophy and osteopenia.Acta neuropathologica communications · 2026Article
- γδ T cell-derived IL-4 initiates CD8Nature immunology · 2026Article
- Antigen reactivity defines tissue-resident memory and exhausted T cells in tumors.Nature immunology · 2026Article
- Removal of unwanted variation in pseudobulk analysis of single-cell RNA sequencing data and the leveraging of pseudoreplicates.NAR genomics and bioinformatics · 2025Article
- A 107 Gene Nanostring Assay Effectively Translates the Cancer Genome Atlas, and Tumour Microenvironment Gastric Cancer Molecular Classification to a Patient-Derived Organoid Model.Genes, chromosomes & cancer · 2025Article
- Per- and polyfluoroalkyl substances (PFAS) and microRNA: An epigenome-wide association study in firefighters.Environmental research · 2025Article
- Pathway metabolite ratios reveal distinctive glutamine metabolism in a subset of proliferating cells.Molecular systems biology · 2025Article
- Tissue gene expression analysis approach in a context of high technical and biological heterogeneity.BMC research notes · 2025Article
- shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data.Bioinformatics (Oxford, England) · 2025Article
- DNA-damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease.iScience · 2025Article
- Stem-like memory and precursors of exhausted T cells share a common progenitor defined by ID3 expression.Science immunology · 2025Article
- Proteomic and metabolomic analyses of the human adult myocardium reveal ventricle-specific regulation in end-stage cardiomyopathies.Communications biology · 2024Article
- Challenges and opportunities in processing NanoString nCounter data.Computational and structural biotechnology journal · 2024Review
- Beyond-local neural information processing in neuronal networks.Computational and structural biotechnology journal · 2024Article
- Semisynthetic simulation for microbiome data analysis.Briefings in bioinformatics · 2024Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These counts need to be normalized to adjust for the amount of sample, variations in assay efficiency and other factors. Most users adopt the normalization approach described in the nSolver analysis software, which involves background correction based on the observed values of negative control probes, a within-sample normalization using the observed values of positive control probes and normalization across samples using reference (housekeeping) genes. Here we present a new normalization method, Removing Unwanted Variation-III (RUV-III), which makes vital use of technical replicates and suitable control genes. We also propose an approach using pseudo-replicates when technical replicates are not available. The effectiveness of RUV-III is illustrated on four different datasets. We also offer suggestions on the design and analysis of studies involving this technology.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.