ArticleCancer informatics2013
An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma Study.
Article in Cancer informatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Article
- The validity of circulating microRNAs in oncology: five years of challenges and contradictions.Molecular oncology · 2014Review
- MicroRNA array normalization: an evaluation using a randomized dataset as the benchmark.PloS one · 2014Article
- Circulating cell-free microRNA as biomarkers for screening, diagnosis and monitoring of neurodegenerative diseases and other neurologic pathologies.Frontiers in cellular neuroscience · 2013Review
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3 authors.
Funding
Abstract
backgroundMethods for array normalization, such as median and quantile normalization, were developed for mRNA expression arrays. These methods assume few or symmetric differential expression of genes on the array. However, these assumptions are not necessarily appropriate for microRNA expression arrays because they consist of only a few hundred genes and a reasonable fraction of them are anticipated to have disease relevance.
methodsWe collected microRNA expression profiles for human tissue samples from a liposarcoma study using the Agilent microRNA arrays. For a subset of the samples, we also profiled their microRNA expression using deep sequencing. We empirically evaluated methods for normalization of microRNA arrays using deep sequencing data derived from the same tissue samples as the benchmark.
resultsIn this study, we demonstrated array effects in microRNA arrays using data from a liposarcoma study. We found moderately high correlation between Agilent data and sequence data on the same tumors, with the Pearson correlation coefficients ranging from 0.6 to 0.9. Array normalization resulted in some improvement in the accuracy of the differential expression analysis. However, even with normalization, there is still a significant number of false positive and false negative microRNAs, many of which are expressed at moderate to high levels.
conclusionsOur study demonstrated the need to develop more efficient normalization methods for microRNA arrays to further improve the detection of genes with disease relevance. Until better methods are developed, an existing normalization method such as quantile normalization should be applied when analyzing microRNA array data.
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