[BioC] RMA normalization, which samples should be normalized together

[Arne.Muller at sanofi-aventis.com]

Dear Johannes,

I've a study with 84 affy chip to characterize a dose effect of a drug. The study was conducted in 3 different laboratories. There are strong differences betweent the laboratories and I've RMA normalized per laboratory and then merged the results in a single linear moel including the laboratory as an additional factor. Maybe you can make the patient or source of RNA a random factor in a mixe effects model - if you've replication per patient.

Just looking at those genes with a significant dose effect I did not find much differences between normalizing all chips together and  normalizing per laboratory.

	regards,

	Arne


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Dipl.-Ing.
> Johannes Rainer
> Sent: 07 February 2005 10:13
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] RMA normalization,which samples should be normalized
> together
> 
> 
> hi,
> we are interested in the response of patients to a special treatment, 
> so we have patient samples before and after treatment. i have 
> normalized this samples in different ways using RMA. As RMA tries to 
> detect and correct probe effects by looking at the expresison 
> levels of 
> the probes across all chips it is not surprising that the outcome of 
> the analysis differs depending on which chips i normalize together.
> It is clear that i have to normalize all patient samples 
> together if i 
> want to compare the expression values of the genes (lets say using 
> statistical tests). i am also analyzing the chips using the 'old 
> fashioned way' by using M and A values and i suppose it is not 
> problematic at all to compare M values of lets say patient 1, 6 hours 
> sample against 0 hours sample with those from patient 2, also 6 hours 
> versus 0 hours where the chips from the two patients were NOT 
> normalized together.
> 
> -now my question is if someone else has experience in what samples 
> could and should be normalized together with RMA. I saw that ther are 
> (big) differences in the regulation (M) values if i normalize two 
> different patients together compared with the values that i 
> get when i 
> normalize only samples from the same patients together.
> 
> thanks in advance
> 
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