Platform Comparison for miRNA
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ABSTRACT: The goal of this study was to investigate the generation and normalization of microRNA expression data based on microarray technologies to comparatively assess their quality. Two profiling platforms were compared: the single-channel Affymetrix GeneChip(r) and the Exiqon dual-channel miRCURY LNA(tm), which was processed as a single-channel array. Due to fundamental differences in the platform constitution, the normalization methods developed for gene expression need to be applied very cautiously to microRNA raw data. This motivated the development of a novel normalization method based on controllable assumptions, which uses the intensities of spike-in control probes. The results showed that the novel normalization method reduced the data variability in the most consistent way and confirmed the reliability of the differentially expressed microRNAs obtained, based on an RT-qPCR experiment performed for a subset of microRNAs. The conclusion was that the Exiqon platform combined with the novel spike-in controls based normalization method provides high-quality microRNA expression data suitable for reliable downstream analysis. This preprocessing pipeline was implemented into an R package called ExiMiR and deposited in the Bioconductor repository. The Exiqon data set has also been deposited in ArrayExpress under accession number E-MTAB-876.
INSTRUMENT(S): Affymetrix GeneChip Scanner 3000 7G
ORGANISM(S): Mus musculus
SUBMITTER: Sam Ansari
PROVIDER: E-MTAB-875 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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