Hi Pingzhao,

Thanks for your mail.

You wrote:
> ...  Say you have two data sets A (affy) and B (cDNA). Early stage: first
normalize data sets A and B, separately; then somehow rescale normalized A
and B; finally put them together

I think you missed the point in my mail. The issue I mentioned was a bit
different. Taking your example, for data set A, I have got A1 & A2 - which
come from two chip-types (similarly, I have got B1, B2 & B3 from three cDNA
print-layouts, i.e., 3 GAL files ).

Then, I'm looking into (suitable ways &/or packages for) merging of A1 & A2
in a correct way to form ONE normalized file  => A
[And, similarly to merge, B1, B2 & B3 to form ONE file  => B]

Kathy

PS: I also thank for all the comments received [including the recent
messages from Laurent and Adai].


 == = = = = = = =


>
> 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@sickkids.ca
> Web: http://www.tcag.ca/statisticalAnalysis.html
>

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