FW: [BioC] normalize by or across all treatments

[Stephen Henderson]

-----Original Message-----
From: Stephen Henderson 
Sent: Monday, June 16, 2003 4:02 PM
To: 'Park, Richard'
Subject: RE: [BioC] normalize by or across all treatments

I somewhat disagree--If you have meaningful contrasts (with 3 replicates)
they will survive normalising all together. 

If you normalise separately you will almost certainly introduce false
differences- and if you then try lots of ways you might find some you like.

Stephen

-----Original Message-----
From: Park, Richard [mailto:Richard.Park at joslin.harvard.edu] 
Sent: Monday, June 16, 2003 3:56 PM
To: Leanna House; bioconductor
Subject: RE: [BioC] normalize by or across all treatments

These are my two cents to the question. I would at first normalize
everything together via rma, which does poses risks of diminishing or
enhancing treatment effects. But I believe this would allow you to see the
overall picture of the data and give you a general sense of how each
treatment compares to each other and the control. 

And if you wanted to spend some more time, you could then try creating
various data sets by using rma to normalize data between each treatment and
the control and have 4 groups of data (each treatment normalized w/ the
control). This would be a more specific analysis leaving out the enhancing
or diminishing effects of normalization between many different treatments. 

Richard Park 

-----Original Message-----
From: Leanna House [mailto:house at stat.duke.edu]
Sent: Monday, June 16, 2003 10:25 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] normalize by or across all treatments


In replicates of 3, I have a set of control and 4 treatment arrays.  My
question is, do I normalize (via rma) using all of the arrays at once, or
do I normalize by treatment.  I have asked other reliable sources and have
received conflicting responses.  I feel the issue is that, in one case, I
may, if not completely wipe out, severely diminish any possible treatment
effects, whereas, in the other case, I may actually induce a treatment
effect.  Any thoughts?

Thank you so much,
Leanna

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