Sent from a cell phone, please excuse typos and terseness.
On Nov 3, 2013 3:04 AM, <bioc-devel-request@r-project.org> wrote:

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>    1. Re: lumiT VST Normalisation Fails (Dario Strbenac)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 3 Nov 2013 04:00:49 +0000
> From: Dario Strbenac <dstr7320@uni.sydney.edu.au>
> To: Pan Du <dupan.mail@gmail.com>
> Cc: "bioc-devel@r-project.org" <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] lumiT VST Normalisation Fails
> Message-ID:
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> 0000b1a39f01485eae1c874c83d717c4@BLUPR01MB035.prod.exchangelabs.com>
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> I read the journal article about the variance stabilizing method. I
> understand how it uses the p-value in its algorithm now. Some better error
> checking and message to the user would be useful, if the user created the
> object with new() from IDAT files. I will ask for the data to be exported
> again, with the necessary columns. It's also missing the number of beads
> column.
>
> ________________________________
> From: du4pan1@gmail.com <du4pan1@gmail.com> on behalf of Pan Du <
> dupan.mail@gmail.com>
> Sent: Saturday, 2 November 2013 3:31 AM
> To: Dario Strbenac
> Cc: bioc-devel@r-project.org
> Subject: Re: lumiT VST Normalisation Fails
>
> Hi Dario
>
> You are correct that the LumiBatch class only requires exprs and se.exprs.
> But for VST transform in lumiT, the detection p-values will help it better
> estimates the transformation. (For user flexibility, I will make it also
> accepts LumiBatch without detection matrix.)
>
> As for the SampleIDs, which are the prefix of column names to identify
> samples in the Illumina BeadStudio/GenomeStudio output file.  The vignette
> lumi.pdf has some example plots. In order to match controlData file with
> expression data file, these column headers should match up.
>
> Pan
>
>
> On Thu, Oct 31, 2013 at 11:00 PM, Dario Strbenac <
> dstr7320@uni.sydney.edu.au<mailto:dstr7320@uni.sydney.edu.au>> wrote:
> Hello,
>
> I have a LumiBatch object, but the lumiT function produces an error.
>
> > class(treatmentBatch)
> [1] "LumiBatch"
> attr(,"package")
> [1] "lumi"
> > treatmentBatch <- lumiT(treatmentBatch)
> Perform vst transformation ...
> Error in !assayDataValidMembers(assayData(x.lumi), "detection") :
>   invalid argument type
>
> Since I've created a valid object of class LumiBatch, it should work on
> that object without errors. In fact, the documentation of the class states
> : "The arguments to new should include exprs and se.exprs, others can be
> missing, in which case they are assigned default values." Nothing in the
> documentation of lumiT states that detection p-values are required, so it's
> a mystery to the lumi end-user what obscure format of parameters the
> package author expects them to provide.
>
> Another example of this type of problem is
>
> > treatmentBatch <- addControlData2lumi(controlTable, treatmentBatch)
> Error in addControlData2lumi(controlTable, treatmentBatch) :
>   SampleID does not match up between controlData and x.lumi!
>
> controlData is described as "a data.frame with first two columns as
> "controlType" and "ProbeID". The rest columns are the expression amplitudes
> for individual samples." Searching the entire PDF manual of the help pages
> also does not show SampleID described anywhere.
>
> I am using lumi 2.14.0.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
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> End of Bioc-devel Digest, Vol 116, Issue 3
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