ArticleNucleic acids research2013
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 2 of them syntheses that pooled it.
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
66 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells.PloS one · 2016Pooled it
- Robust meta-analysis shows that glioma transcriptional subtyping complements traditional approaches.Cellular oncology (Dordrecht, Netherlands) · 2014Pooled it
- Inhibition of β-Catenin Signaling in the Skin Rescues Cutaneous Adipogenesis in Systemic Sclerosis: A Randomized, Double-Blind, Placebo-Controlled Trial of C-82.The Journal of investigative dermatology · 2017Trial
- Temporal changes in gene regulation during human tissue repair.Scientific reports · 2026Article
- Loss of ten-eleven translocation 2 (TET2) facilitates aggressive behaviour in cutaneous melanoma by inducing peroxisome proliferator-activated receptor-γ coactivator 1α expression and oxidative phosphorylation.The British journal of dermatology · 2026Article
- A novel insight into neurological disorders through HDAC6 protein-protein interactions.Scientific reports · 2024Article
- Over-expression of mir-181a-3p in serum of breast cancer patients as diagnostic biomarker.Molecular biology reports · 2024Article
- Article
- Omada: robust clustering of transcriptomes through multiple testing.GigaScience · 2024Article
- Transcriptional changes in human palate and skin healing.Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society · 2023Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Microarray Data Preprocessing: From Experimental Design to Differential Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts.International journal of molecular sciences · 2021Article
- Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis.Genes & nutrition · 2021Review
- CCR2 improves homing and engraftment of adipose-derived stem cells in dystrophic mice.Stem cell research & therapy · 2021Article
- Selenotranscriptome Network in Non-alcoholic Fatty Liver Disease.Frontiers in nutrition · 2021Article
- Article
- Comprehensive analysis reveals a six-gene signature and associated drugs in mimic inguinal hernia model.Hernia : the journal of hernias and abdominal wall surgery · 2020Article
- Article
- Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data.Nanomaterials (Basel, Switzerland) · 2020Review
6 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
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.
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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 OpenQuestion graph.