p Sent from a cell phone, please excuse bypos and terseness. On Nov 3, 2013 3:04 AM, <bioc-devel-requ...@r-project.org> wrote:
> Send Bioc-devel mailing list submissions to > bioc-devel@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioc-devel > or, via email, send a message with subject or body 'help' to > bioc-devel-requ...@r-project.org > > You can reach the person managing the list at > bioc-devel-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioc-devel digest..." > > > Today's Topics: > > 1. Re: lumiT VST Normalisation Fails (Dario Strbenac) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 3 Nov 2013 04:00:49 +0000 > From: Dario Strbenac <dstr7...@uni.sydney.edu.au> > To: Pan Du <dupan.m...@gmail.com> > Cc: "bioc-devel@r-project.org" <bioc-devel@r-project.org> > Subject: Re: [Bioc-devel] lumiT VST Normalisation Fails > Message-ID: > < > 0000b1a39f01485eae1c874c83d71...@blupr01mb035.prod.exchangelabs.com> > Content-Type: text/plain > > 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: du4p...@gmail.com <du4p...@gmail.com> on behalf of Pan Du < > dupan.m...@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 < > dstr7...@uni.sydney.edu.au<mailto:dstr7...@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 > > > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > Bioc-devel mailing list > Bioc-devel@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > End of Bioc-devel Digest, Vol 116, Issue 3 > ****************************************** > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
