ArticleNucleic acids research2013
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Trial
- C4B gene influences intestinal microbiota through complement activation in patients with paediatric-onset inflammatory bowel disease.Clinical and experimental immunology · 2017Trial
- Trial
- A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.Briefings in bioinformatics · 2023Article
- Does entry to center-based childcare affect gut microbial colonization in young infants?Scientific reports · 2020Article
- Article
- Identification of COL1A1 as an invasion‑related gene in malignant astrocytoma.International journal of oncology · 2018Article
- Gut Microbiota and Body Weight in School-Aged Children: The KOALA Birth Cohort Study.Obesity (Silver Spring, Md.) · 2018Article
- Rotavirus vaccine response correlates with the infant gut microbiota composition in Pakistan.Gut microbes · 2018Article
- Article
- Article
- Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation.The American journal of gastroenterology · 2015Article
- Fat, fibre and cancer risk in African Americans and rural Africans.Nature communications · 2015Article
- A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.Skeletal muscle · 2015Article
- Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.PloS one · 2015Article
- Tipping elements in the human intestinal ecosystem.Nature communications · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid accumulation of large and standardized microarray data collections is opening up novel opportunities for holistic characterization of genome function. The limited scalability of current preprocessing techniques has, however, formed a bottleneck for full utilization of these data resources. Although short oligonucleotide arrays constitute a major source of genome-wide profiling data, scalable probe-level techniques have been available only for few platforms based on pre-calculated probe effects from restricted reference training sets. To overcome these key limitations, we introduce a fully scalable online-learning algorithm for probe-level analysis and pre-processing of large microarray atlases involving tens of thousands of arrays. In contrast to the alternatives, our algorithm scales up linearly with respect to sample size and is applicable to all short oligonucleotide platforms. The model can use the most comprehensive data collections available to date to pinpoint individual probes affected by noise and biases, providing tools to guide array design and quality control. This is the only available algorithm that can learn probe-level parameters based on sequential hyperparameter updates at small consecutive batches of data, thus circumventing the extensive memory requirements of the standard approaches and opening up novel opportunities to take full advantage of contemporary microarray collections.
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