[BioC] Format NCprobe index file gcrma

[Zhijin (Jean) Wu]

The NCprobe is a vector of indexes for control probes.

For example, let "object" be your AffyBatch or oligo object, if you do
    intensity(object)[NCprobe,]
you will get the intensities of the control probes.

You may need function "xy2i" to get the index if you start from the x and 
y 
coordinates of your control probes.

best,
Jean Wu



On Wed, 28 Mar 2007, Hans van Leeuwen wrote:

> Hi,
>
> I would like to use my own set of negative control probes with gcrma. I
> can't find an example or explanation with the format of the NCprobe index
> file in the function description or gcrma instructions.
>
> Is it just a file with the x and y coordinates in columns? Does the
> bg.adjust.gcrma function read the file directly, or do I need to read the
> file first and create an object?
>
> Thanks for any help.
>
> Best,
>
> Hans van Leeuwen
>
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