title: Modified least-variant set normalization for miRNA microarray.
abstract: MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional regulation of mRNAs. Microarrays have been employed to measure global miRNA expressions; however, because the number of miRNAs is much smaller than the number of mRNAs, it is not clear whether traditional normalization methods developed for mRNA arrays are suitable for miRNA. This is an important question, since normalization affects downstream analyses of the data. In this paper we develop a least-variant set (LVS) normalization method, which was previously shown to outperform other methods in mRNA analysis when standard assumptions are violated. The selection of the LVS miRNAs is based on a robust linear model fit of the probe-level data that takes into account the considerable differences in variances between probes. In a spike-in study, we show that the LVS has similar operating characteristics, in terms of sensitivity and specificity, compared with the ideal normalization, and it is better than no normalization, 75th percentile-shift, quantile, global median, VSN, and lowess normalization methods. We evaluate four expression-summary measures using a tissue data set; summarization from the robust model performs as well as the others. Finally, comparisons using expression data from two dissimilar tissues and two similar ones show that LVS normalization has better operating characteristics than other normalizations.
authors.affiliation: Centre for Molecular Epidemiology, National University of Singapore, 117597 Singapore.
authors.forename: Chen
authors.initials: C
authors.lastname: Suo
authors.forename: Agus
authors.initials: A
authors.lastname: Salim
authors.forename: Kee-Seng
authors.initials: KS
authors.lastname: Chia
authors.forename: Yudi
authors.initials: Y
authors.lastname: Pawitan
authors.forename: Stefano
authors.initials: S
authors.lastname: Calza
mesh_terms: D000704:Analysis of Variance; D001921:Brain / Q000378:metabolism; D004526:Efficiency; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards* / Q000706:statistics & numerical data; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D015233:Models, Statistical; D018482:Muscle, Skeletal / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards* / Q000706:statistics & numerical data; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D046888:Tissue Array Analysis / Q000379:methods / Q000592:standards / Q000706:statistics & numerical data
chemical_list: D035683:MicroRNAs