[BioC] beadarray controlProfile

[Mark Dunning]

Hi,

Control information for current expression platforms is stored in the
ExpressionControlData object in beadarray.

>data(ExpressionControlData)
> names(ExpressionControlData)
[1] "Humanv3"   "Humanv2"   "Humanv1"   "Mousev2"   "Mousev1"   "Mousev1p1"
[7] "Ratv1"     "Humanv4"

> head(ExpressionControlData[["Humanv3"]])
  Array_Address Reporter_Group_Name Reporter_Group_Identifier
1       4730189            negative         permuted_negative
2       5700037            negative         permuted_negative
...

The controlProfile object is specifically for the example dataset
supplied with the package (it is indeed a very old dataset). It is
also example of how users with data other than the standard platforms
listed in ExpressionControlData can use the functions in the pacakge.
If you have set the annotation of the beadLevelData object when you
use readIllumina, or later with setAnnotation, then this control
information should be available to the plotting and summarisation
functions.

Hope this helps,

Mark

On Wed, Nov 3, 2010 at 10:02 PM, Ying W <daiyingw at gmail.com> wrote:
> Hi,
> I am following the 'Analysis of Bead-level Data using beadarray' from
> beadarray bioconductor page.
>
> I am at the controlProbe step and it seems like the data(controlProfile)
> command brings up information for a very old version of beadArray (only 76
> control probes).
> I was wondering where I could get the PROBE_IDs for the newer control probes
> especially for platforms HuRef8v3 and HumanHT12v4.
> Do PROBE_IDs change between v3 and v4?
> Lastly, is there a place to find the 'Reference Manuals' in TeX instead of
> pdf? I ask because sometimes parameters are cut off and also would make
> things easier to grep.
>
> Thanks,
> Ying Wu
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>