[BioC] create CNA object in DNAcopy package with agilent data

[Sean Davis]

jhs1jjm at leeds.ac.uk wrote:
> Sean,
>
> Awesome, seems to have worked. There were 2 warnings, NAs introduced by
> coercion. Just changed the end (after messing around with importing the raw
> data) to the marray object as follows:
>
> agilentInfo <- extractAgilentInfo(as.character(mnorm at maGnames@maInfo[,3]))
>
> Guessing that would have taken me a while to work out. Is there any reason why
> this wouldn't work for the 244k array just for future reference? Will try start
> the DNAcopy analysis now.
>   

John,

Great to hear that it worked for you.  The NAs introduced are expected 
and are associated with the control probes on the array.  It should work 
just fine for all Agilent arrays as long as the systematic name is in 
the same format.  Agilent is actually pretty good about keeping things 
stable over different arrays and over time.

Sean

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