[BioC] comparing different experiments

[Julia Engelmann]

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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