[BioC] processCGH with snapCGH

Sean Davis sdavis2 at mail.nih.gov
Fri Sep 28 20:08:34 CEST 2007


>>> ord <- order(MA$genes$Chr, MA$genes$Position)
>>> I'm not sure where the variable MA$genes$Postion has come from as
>>> readPositionalInfo didn't create it.
>> Hi, John.
>>
>> Try:
>>
>> colnames(MA1$genes)[10] <- 'Position'
>>
>> Then rerun processCGH.
>>
>> Sean
>>
> Hi Sean,
> 
> I did the following:
> 
>> MA1$genes$Position <- MA1$genes$Start
> 
> i.e what you said I think and it worked. Was it just a problem with the
> function or have I missed a step somewhere?

The readPositionalInfo names the columns Chr, Start, and End.  Position
is needed by processCGH, so the functions do not work well together.

Sean



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