[BioC] Data analysis

Gordon Smyth smyth at wehi.edu.au
Fri Oct 17 06:40:54 MEST 2003

At 11:53 PM 16/10/2003, Jason Skelton wrote:
>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 
>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 haven't implemented this in limma because it seems to me that it might 
invalidate the assumptions behind the duplicate correlation approach. See 
the earlier post:


>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  ;-)

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