ArticleBioinformatics (Oxford, England)2013
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Gene expression profiling of sequential metastatic biopsies for biomarker discovery in breast cancer.Molecular oncology · 2015Trial
- Curated and harmonised transcriptomics datasets of interstitial lung diseases.Data in brief · 2025Article
- The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis.Human genomics · 2022Article
- Genome-scale meta-analysis of breast cancer datasets identifies promising targets for drug development.Journal of biological research (Thessalonike, Greece) · 2021Article
- Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients.Scientific data · 2020Article
- Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data.Nanomaterials (Basel, Switzerland) · 2020Review
- Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions.Microbiology and molecular biology reviews : MMBR · 2018Review
- Article
- Immunological landscape of consensus clusters in colorectal cancer.Oncotarget · 2017Article
- Microarray experiments and factors which affect their reliability.Biology direct · 2015Review
- Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data.Microarrays (Basel, Switzerland) · 2014Article
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Authors and funding
2 authors.
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Abstract
motivationGene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here. AVAILABILITY: The package is available via Bioconductor at the URL http://bioconductor.org/packages/release/bioc/html/AffyRNA Degradation.html
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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 OpenQuestion graph.