[BioC] MANOR and MySQL

[Pierre Neuvial]

Hi James,

As for your first question, I have not done anything like this before. In our software CAPweb which includes normalisation with MANOR, we work with text files only.

I can answer your 2nd question: it is possible. The creation of arrayCGH objects is documented (in the GLAD package, see ?arrayCGH). What you need to create an arrayCGH object is a data.frame 'arrayValues' with reporter-level (spot-level) information, and a vector 'arrayDesign' which specifies the block/spot design of the array.

  a <- list(arrayValues=arrayValues, arrayDesign=arrayDesign)
  class(a) <- "arrayCGH"

In order to perform normalisation within MANOR you should add to this object a data.frame 'cloneValues' containing annotation information for the probes. 'cloneValues' and 'spotValues' should have a common column name that will be used to merge 'arrayValues' and 'cloneValues', say "id":

  a$cloneValues <- cloneValues
  a$ir.rep <- "id"

Hope this helps,

Pierre.

James Morris wrote:
> Hello,
> 
> I would like to able to run a MANOR normalisation from data retrieved from a database, 
> 
> could anybody tell me if they have done anything like this before?
> 
> also is it even possible to create an MANOR arrayCGH object without a file?
> 
> Thanks 
> 
> James 
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