Question: Merging microarray datasets

0

pingzhao Hu •

**210**wrote:
Kathy,
To answer your questions, you may need to know which stages you are
trying to integrate your data sets.
Roughly speaking, data sets can be integrated at three stages:
Say you have two data sets A (affy) and B (cDNA)
(1) early stage: first normalize data sets A and B, separately; then
somehow rescale normalized A and B; finally put them together
(2) middle level stage; first normalize data sets A and B, then
calculate effect size (or like meansures/methods) for each gene in A
and B, separately;
finally you can use random/fixed effects model to integrate the
effect sizes (like Choi et al. 2003 method)
(3) late stage: first calculate normalize data sets A and B,
separately; calculate p-value/test statistic for each gene in each
study (standard methods used
in single study); finally combine the p-values (say using Fisher
method)/test-statistic.
There are some bioconductor packages can do (2) and (3) -like
RankProd.
Pingzhao
========================================
Pingzhao Hu
Statistical Analysis Facility
The Centre for Applied Genomics (TCAG)
The Hospital for Sick Children Research Institute
MaRS Centre - East Tower
101 College Street, Room 15-705
Toronto, Ontario, M5G 1L7, Canada
Tel.: (416) 813-7654 x6016
Email: phu at sickkids.ca
Web: http://www.tcag.ca/statisticalAnalysis.html