[BioC] MANOR and MySQL
pierre.neuvial at curie.fr
Fri May 18 11:26:12 CEST 2007
Sorry, I meant 'id.rep', not 'ir.rep', see below...
Pierre Neuvial wrote:
> 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"
a$id.rep <- "id"
> Hope this helps,
> James Morris wrote:
>> 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?
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