[BioC] Illumina chip analysis - normalisation

[Wei Shi]

Dear Yogi:

    I think you should do the normalization for the two chips instead of 
normalizing them separately. Given the two chips were hybridized at 
different time, I would expect there is obvious difference between the 
two chips (you can check this using boxplot). The between-array 
normalization across the two chips can help remove this difference.

    Hope this helps.

Cheers,
Wei

Yogi Sundaravadanam wrote:
> Hi all,
>
>  
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> Do you think it is good to normalize two illumina chips (done months
> apart) together? Or do I normalize the chips separately?
>
>  
>
> Any suggestions would be very helpful
>
>  
>
> Thanks 
>
> Yogi 
>
>  
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