[BioC] Data analysis
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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