[BioC] SimpeAffy: how to get/generate qcdef file?

[Renaud Gaujoux]

Hi,

I actually read the vignette but how do you get all the information 
needed to create the file? I guess the qcdef file showed in vignette 
will not work as it is for a sugar cane array (even changing the header 
name to sugarcanecdf).

Do I have to look by eye at the cdf file and extract the info? In that 
case how do I know which control probe to chose? all of them?
It seems to me that the kind of information required can be found 
automatically. I am not familiar with the Affy cdf format so I find it a 
bit tricky to do that by hand.
Is there some procedure to follow to find the correct information in the 
file?

Thanks.
Renaud

claire wilson wrote:
> Hi Renaud
>
> see page 13 of the vignette for details on how to create a qcdef file
>
> http://bioconductor.org/packages/2.3/bioc/vignettes/simpleaffy/inst/doc/simpleAffy.pdf
>
> hth
>
> claire