[BioC] lumi: how is the controlData to be read and used?

[Gordon Smyth]

At 10:00 AM 30/10/2007, Pan Du wrote:
>Hi Gordon,
>
>Sorry for replying late. I think that should work because the
>Control_Gene_Profile.txt file basically averaged the negative control
>probes. As described in the BeadStudio manual, its background adjustment
>basically subtact the mean of negative control probes. But I am not sure
>whether BeadStudio did outlier removal or not. Anyway, the results should be
>close.

Thanks.

>Also I will update lumiR function (or write a new function) to read the
>Control_Probe_Profile.txt because the negative control probes have the same
>probe Ids.

Actually, the ProbeIDs are all different for the negative controls. 
It is the TargetIDs which are the same.

Repetition of ProbeIDs only occurs when the same probe can be 
classified as more than one type of control (for example mouse probe 
60019 is both a cy3_hyb control and a low_stringency_hyb control).

Best wishes
Gordon

>Thanks!
>Pan