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

[Gordon Smyth]

At 08:11 AM 28/10/2007, Pan Du wrote:
>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.

I am glad that you are open to opinions, but it is disconcerting that 
you are not prepared to make any recommendations about background correction.

This leaves me wondering how to use the lumi package at the moment. 
The results from vst do change somewhat depending on how the data has 
been background corrected. If you're not making any recommendations 
about background correction, does this mean that you're not yet ready 
to recommend vst either?

Are you saying that background correction makes so little difference 
that vst can be recommended regardless of the background correction method?

Or are you saying that the pre-processing methods of the lumi package 
are in general not yet fully developed or tested, so that we should 
not view them as recommendations?

>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.

No, this does not work, for several reasons.

Firstly, there is no slot called "controlProbe". I think you mean 
"controlData".

Secondly, there is no slot called "exprs". I think you mean the 
exprs() extractor function.

Thirdly, exprs(x) is a matrix, whereas the controlData slot has to be 
a data.frame.

Fourthly, and most serious, when lumiR() reads a control probe 
profile, exprs(x) loses any information on which probes are negative 
controls, making it completely useless for background correction. The 
row names are just probeID numbers:

   > x <- lumiR(file.path("data","Actn3_Control_Probe_Profile.txt"))
   Warning message:
   In lumiR(file.path("data", "Actn3_Control_Probe_Profile.txt")) :
     Duplicated IDs found and were merged!
   > rownames(exprs(x))[1:5]
   [1] "610064"    "100610064" "100580056" "580056"    "360035"

As I said, a complete code example would be helpful!

Gordon

>Thanks!
>Pan
>
>
> > 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>
> >
> > 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