[BioC] Data analysis

[Jason Skelton]

Gordon Smyth wrote:

>
> I would use the limma commands lmFit (or lm.series or gls.series) 
> followed by makeContrasts, eBayes and classifyTests. See the earliers 
> posts:
>
Thanks for this infomation Gordon I'll try this and see what results I get.........

On a different note 

The arrays I have tested LIMMA on have 2 duplicates and are spaced evenly throughout the array and so have no problems running your functions.

Someone else at the Sanger Insitite would like to be able to use LIMMA but the number of duplicates for each gene differs on their array e.g for some genes their are two copies and for others there would be four copies or more which inturn obviously effects spacing etc between replicates.  
I'm not sure why they would want differing numbers of copies of genes but they would like to be able to estimate the correlation between these genes anyway and obviously see the results as one data point per merged gene.

I've tried to think of how this can be done but it seems overly complex and I'm not sure if it is at all possible in R or Limma.

I'm guessing there is no way of carryout the correlation, series model fits etc based simply on the "Name" specified in the GAL files ?
or some how specifying the duplicate number for each gene seperately
and somehow merging this information for use as a parameter ?

I'm doubting very much that this can be done at all but it's worth asking  ;-)

thanks

Jason



-- 
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Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919