Journal article
Separate-channel analysis of two-channel microarrays: Recovering inter-spot information
GK Smyth, NS Altman
BMC Bioinformatics | BMC | Published : 2013
Abstract
Background: Two-channel (or two-color) microarrays are cost-effective platforms for comparative analysis of gene expression. They are traditionally analysed in terms of the log-ratios (M-values) of the two channel intensities at each spot, but this analysis does not use all the information available in the separate channel observations. Mixed models have been proposed to analyse intensities from the two channels as separate observations, but such models can be complex to use and the gain in efficiency over the log-ratio analysis is difficult to quantify. Mixed models yield test statistics for the null distributions can be specified only approximately, and some approaches do not borrow streng..
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Awarded by National Science Foundation
Funding Acknowledgements
Gordon Smyth is grateful for discussions with Natalie Thorne. Gordon Smyth's research was supported by Program Grants 257501 and 257529 from the National Health and Medical Research Council (NHMRC). This work was also made possible by Victorian State Government Operational Infrastructure Support and the NHMRC Independent Research Institute Infrastructure Support Scheme. Naomi Altman's work was supported in part by NSF DMS 1007801 and by NIH UL1RR033184. Naomi Altman's work was also partially supported by the National Science Foundation under Grant DMS-1127914 to the Statistical and Applied Mathematical Sciences Institute. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.