expression array normalization and different comparisons: an only "total" normalization or a normalization per comparison?
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boczniak767 ▴ 720
@maciej-jonczyk-3945
Last seen 2 days ago
Poland
Dear Ana, > Dear list: > > I have a question about how to do expression microarray normalization > when > doing group > comparisons. I have 40 individuals (20 cases, 20 controls) and each > one has > 3 > mRNA chips at different time-points. Should I normalize all the chips > (40x3) > together (and the subset for each comparison) or if I am comparing > cases_time1 vs controls_time1, or cases_time1 vs > cases_time2, should I normalize only these 40 chips involved in this > particular comparison? (I am working with Illumina chips) > If that is two colour chips you should normalize your data for each chip separately - so called within array normalization (to correct dye and array specific effects), and then normalize chips together - between array normalization (to make distribution of data from each chip comparable to each other, so you can perform statistical tests). If this arrays are one-colour then only second normalization will be useful. > I am new in the expression analysis and I would appreciate any > comments > about > advantages or disadvantages regardind these two approaches. I **strongly** recommend you to search Illumina's pages for documents about their approach and reccomendations, and then to find appropriate Bioconductor package (which implements recommended procedures and surely will give you sketch of workflow). Of course literature search will be also helpful. HTH, Best Wishes, Maciej Jo?czyk -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
Normalization Normalization • 659 views
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