[BioC] comparing different experiments

Fangxin Hong fhong at salk.edu
Tue Nov 9 22:26:19 CET 2004

> I wonder if I can compare Affymetrix arrays of the same type (ATH1)
> which were made in different laboratories and with different tissue
> types and different references. I have: "tissue1 treated", "tissue1
> untreated" from one lab and "tissue2 treated", "tissue2 untreated" from
> the other lab.
> The references (untreated) are  different because of the different
> tissue types. I am interested in the difference between tissue1 treated
> and tissue2 treated, so I thought I could use limma to make a contrast:
> (tissue1_treated-tissue1_untreated)-(tissue2_treated-tissue2_untreated).
> I am not sure if this is valid, though? For example, I do not account
> for the different labs that way.
> Maybe it is just possible to analyse each experiment by itself and
> compare the results at a latter stage, say compare lists of
> differentially expressed genes?
Based on what I observed when study data generated at different lab, lab
effect can't not be completely removed by normalization step. If you do
have some replicates or several data sets from each lab, and you want to
combine data together, I would suggest you to inlcude a fixed effect for
lab factor.
Hopefully this will help.


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Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu

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