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

[Pan Du]

Hi Gordon,

The using of controlProbe data has not been well developed yet. Actually we
would like to hear the opinions from you and other developers about how to
using control probe information.
The Control_Probe_profile.txt file can also be read by lumiR function. But
the user has to manually extract the exprs slot and add it into the
controlProbe slot. We will further develop on this part.
Thanks!

Pan


On 10/27/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 24
> Date: Sat, 27 Oct 2007 15:12:04 +1000
> From: Gordon Smyth <smyth at wehi.EDU.AU>
> Subject: [BioC] lumi: how is the controlData to be read and used?
> To: "BioC Mailing List" <bioconductor at stat.math.ethz.ch>
> Cc: Wei Shi <shi at wehi.EDU.AU>, Belinda Phipson <phipson at wehi.EDU.AU>
> Message-ID: <6.2.5.6.1.20071027143740.02d4ab40 at wehi.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> The lumi package functions lumiB() and bgAdjust() mention the fact
> that control data can be used to background correct Illumina data.
> There is however no documentation regarding what the control data
> should contain, how it should be read it in, or exactly how it is used.
> 
> I have summary probe profile data output from BeadStudio (not
> normalized or background corrected):
> 
>    Sample_Probe_Profile.txt
> 
> I also have summary control probe data. This includes both positive
> and negative control probes:
> 
>    Control_Probe_Profile.txt
> 
> How is it recommended that I read and use the control data, prior to
> using lumiT(method="vst")? A complete code example would be helpful.
> 
> Gordon
>