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

[Pan Du]

>> 
>> 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?

What I mean here for the using of control Probe data is using control Probe
information for the quality control information. For the background
adjustment part, currently, we believe using the BeadStudio recommended
method works well. Of course further improvement is possible. The
contribution in this part is very welcome.



>> 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:

We will work on this part later. Because we are busy with other projects, it
may take several weeks. Thanks!


Pan