[BioC] Combining two datasets - help to use GeneMeta.

Gordon Barr gab5 at columbia.edu
Mon Jun 12 16:46:05 CEST 2006


Robert

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?

Thanks

Sincerely,

Gordon

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Developmental Psychobiology
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On Jun 11, 2006, at 2:23 PM, Robert Gentleman wrote:

>
>
> Sean Davis wrote:
>> Sharon wrote:
>>> Hi,
>>>
>>> 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'  
>>> for
>>> 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,  
> these
> 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
>    Robert
>
>>
>> Sean
>>
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>>
>
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
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> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
>
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