comparing different experiments
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@julia-engelmann-559
Last seen 10.2 years ago
Hi list, 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? Any advice, comments or hints are highly appreciated, Julia
limma limma • 973 views
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Fangxin Hong ▴ 810
@fangxin-hong-912
Last seen 10.2 years ago
> 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. Fangxin _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu
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Thank you for the input, Fangxin, but I am not sure if a fixed effect for the lab factor can be modelled in my case, because each lab conducted different experiments, not replicates of the same experiment. Lab 1 did: "tissue1 treated" and "tissue1 untreated" and lab 2 did: "tissue2 treated" and "tissue2 untreated". So I don't see a way to distinguish between lab factor and tissue factor, right? Thanx a lot for any comments, Julia Fangxin Hong wrote: >>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. > >Fangxin > > > >
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