[BioC] Replicates array

[Johannes Freudenberg]

Hi Paola,

For preprocessing I would suggest to use RMA (i.e. RMA background correction + 
quantile normalization + medianpolish) or VSN + medianpolish. I would normalize 
all 6 arrys together. I don't think it's a good idea to normalize the two 
groups separately. 

> Should I just compare the differentially expressed genes lists coming 
> from the two different group of duplicates??

I don't understand. Wouldn't it be just one list?

Johannes



Quoting Paola Sgado' <sgadop at yahoo.it>:

> Hi
> I just started to work with oligonucleotide microarray and I would like
> 
> to have suggestions on the methods I should use to analyse the data.
> 
> I have three duplicates done in two different places, so they look very
> 
> different in terms of background and signal intensities. Since I'm not 
> going to have more duplicates I would like to get the most information 
> possible from these, even if I do know that it is not the perfect 
> experimental design!
> 
> My question is, if the chips are very different, should I normalize 
> them separately (for example make to groups)? Does it make sense to 
> compare them between two gruops if they are normalised separately? 
> Should I just compare the differentially expressed genes lists coming 
> from the two different group of duplicates??
> 
> Thank you for your help!!
> Paola
> 
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