[BioC] Combining two datasets - help to use GeneMeta.
gab5 at columbia.edu
Mon Jun 12 16:46:05 CEST 2006
Could you elaborate a bit on why you think it a bad idea to normalize
separate experiments together. If you normalize each experiment
separately are you requiring the same conditions in each?
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On Jun 11, 2006, at 2:23 PM, Robert Gentleman wrote:
> Sean Davis wrote:
>> Sharon wrote:
>>> I am trying to combine two Affy datasets (on rae230a chips), where
>>> experiments done one year apart. In the first dataset, we have 2
>>> strains with each strain treated and untreated. But for the second
>>> dataset, we have just 2 strains untreated.
>>> Because of unequal levels in the 2 datasets, I am not able to use
>>> 'getdF' in GeneMeta as it is. Any suggestions for using 'getdF'
>>> this situation? or any alternate way of combining these 2 datasets?
>> Are these datasets really that much different that you can't just
>> combine them? They may be, but have you looked at affyPLM results,
>> density plots, etc., just to be sure? If they aren't that much
>> different, perhaps you can just normalize them together and move on?
>> Just asking....
> Sorry, but that is, IMHO, a bad idea. You should never jointly
> normalize separate experiments. Normalize separately and use a random
> effects model for the experiments. As, for how to handle different
> levels of factors/covariates, the issue then becomes one of what
> can be
> estimated from both. Once you identify that you can set up the
> appropriate model and then use tools like nlme and lmer (depending on
> the model) to estimate parameters. But this will require some
> statistical expertise and for that you will have to look locally,
> things are too hard to do over the internet, IMHO.
> There is a BioC technical report on Synthesis of microarray
> experiments that outlines some of these details more completely.
> best wishes
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> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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> rgentlem at fhcrc.org
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