[BioC] Merging microarray datasets

[pingzhao Hu]

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