Yawen Yu, Gaowei Chen, Yang Tao, Xiaofeng Li, Lina Yang, Shengwen Dong
Promoting college students' systems thinking in asynchronous discussions: Encouraging students initiating questions
Frontiers in psychology
preprocessing gene expression data obtained several platforms routinely includes aggregation multiple raw signal intensities one expression value examples computation single expression measure based perfect match pm mismatch mm probes affymetrix technology summarization bead level values bead summary values illumina technology aggregation replicated measurements case technologies including realtime quantitative polymerase chain reaction rtqpcr platforms summarization technical replicates also performed omics disciplines like proteomics metabolomicspreprocessing methods like mas 50 illuminas default summarization method rma vsn show use robust estimators widely accepted gene expression analysis however selection robust methods seems mainly driven high breakdown point efficiency describe optimally robust radiusminimax rmx estimators ie estimators minimize asymptotic maximum risk shrinking neighborhoods ideal model used aggregation multiple raw signal intensities one expression value affymetrix illumina data regard affymetrix data implemented algorithm variant mas 50using datasets literature montecarlo simulations provide reasoning assuming approximate lognormal distributions raw signal intensities means kolmogorov distance least discussed datasets compare results preprocessing algorithms results affymetrixs mas 50 illuminas default methodthe numerical results indicate using rmx estimators accuracy improvement 1020 obtained compared affymetrixs mas 50 15 compared illuminas default method improvement also visible analysis technical replicates reproducibility values terms pearson spearman correlation increased affymetrix almost illumina examples considered algorithms implemented r package named robloxbioc publicly available via cran comprehensive r archive network httpcranrprojectorgwebpackagesrobloxbioc optimally robust rmx estimators high breakdown point computationally feasible lead considerable gain efficiency wellestablished bioinformatics procedures thus increase reproducibility power subsequent statistical analysis