[BioC] xps and unifilter; Error: UnitID not found; error in function ‘ExportData’

[cstrato]

Dear John,

The new version xps_1.8.1 is now available for download. Please let me 
know if this could solve your problem.

Best regards
Christian

On 6/20/10 11:39 PM, cstrato wrote:
> Dear John,
>
> I have just uploaded release version xps_1.8.1 to BioC which should be
> available for download in 1-2 days.
> The reason for the error was that I have forgotten to update internal
> method ExportUnivarTrees() for exon arrays so that it could not find the
> exon probeset annotation data. Thank you for reporting this error.
>
> Best regards
> Christian
>
>
> On 6/19/10 1:35 PM, John Coulthard wrote:
>> Dear Christian
>>
>> Yes. Exactly what I did was...
>>
>> > library(xps)
>> > scheme.HuEx.1.0.st.v2<-import.exon.scheme(filename =
>> "HuEx-1_0-st-v2", layoutfile = "HuEx-1_0-st-v2.r2.clf", schemefile
>> ="HuEx-1_0-st-v2.r2.pgf",
>> probeset="HuEx-1_0-st-v2.na30.hg19.probeset.csv", transcript
>> ="HuEx-1_0-st-v2.na30.hg19.transcript.csv",add.mask=T)
>> > cels =list.files(pattern=".*.CEL")
>> > data.test <- import.data(scheme.HuEx.1.0.st.v2, "tmpdt_DataTest",
>> celdir=".",celfiles=cels, verbose=FALSE)
>> > data.test <- attachInten(data.test)
>> >data.rma <- rma(data.test, filename = "tmpdt_TestRMA", tmpdir =
>> ".",background = "genomic", verbose = FALSE, option="probeset",
>> exonlevel='all')
>> >mvaplot.dev(data.rma, dev = "jpeg", outfile = "RMA.MvAPlot")
>> >mvaplot.dev(data.mas5, dev = "jpeg", outfile = "mas5.MvAPlot")
>> >unifltr <-
>> UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),foldchange=c(1.3,"both"),unifilter=c(0.1,"pval"))
>>
>> >rma.ufr<- unifilter(data.rma, filename="tmpdt_TestUnifilter",
>> filedir=getwd(), filter=unifltr, group = c("a242", "g8", "g8", "g8",
>> "a242", "a242", "g8", "g8", "g8", "a242", "a242", "a242"), verbose = T)
>>
>>
>> Thanks for looking into it for me.
>> John
>>
>> > Date: Fri, 18 Jun 2010 21:18:45 +0200
>> > From: cstrato at aon.at
>> > To: bahhab at hotmail.com
>> > CC: bioconductor at stat.math.ethz.ch
>> > Subject: Re: [BioC] xps and unifilter; Error: UnitID not found; error
>> in function ‘ExportData’
>> >
>> > Dear John,
>> >
>> > I assume that you did "rma(data.exon,...,option="probeset",...)", is
>> > this correct?
>> >
>> > The reason for my question is that I have just tested function
>> > "unifilter()" for the results of rma(...,option="transcript",...) and
>> > rma(...,option="probest",...). In the first case function
>> unifilter() is
>> > ok, however, for the second case I can reproduce the error you get.
>> Thus
>> > I need to investigate and will let you know.
>> >
>> > Best regards
>> > Christian
>> > _._._._._._._._._._._._._._._._._._
>> > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>> > V.i.e.n.n.a A.u.s.t.r.i.a
>> > e.m.a.i.l: cstrato at aon.at
>> > _._._._._._._._._._._._._._._._._._
>> >
>> >
>> > On 6/18/10 10:57 AM, John Coulthard wrote:
>> > >
>> > > Dear list
>> > >
>> > > Can anyone enlighten me to the meaning of this error and how I
>> might get round it?
>> > >
>> > >> rma.ufr<- unifilter(data.rma, ...)
>> > >
>> > > Error: UnitID<322394> not found.
>> > >
>> > > An error has occured: Need to abort current process.
>> > >
>> > > Error in .local(object, ...) : error in function ‘ExportData’
>> > >
>> > >
>> > > More details below
>> > >
>> > > Thanks
>> > > John
>> > >
>> > >> unifltr<-
>> UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),foldchange=c(1.3,"both"),unifilter=c(0.1,"pval"))
>>
>> > >> rma.ufr<- unifilter(data.rma, filename="tmpdt_TestUnifilter",
>> filedir=getwd(), filter=unifltr, group = c("a242", "g8", "g8", "g8",
>> "a242", "a242", "g8", "g8", "g8", "a242", "a242", "a242"), verbose = T)
>> > > Opening file</home/Data/PHD1/HuEx-1_0-st-v2.root> in<READ> mode...
>> > > Creating new temporary
>> file</home/ann/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>...
>> > > Opening file</home/Data/PHD1/tmpdt_TestRMA_20100618_74202.root>
>> in<READ> mode...
>> > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria.
>> > > Opening file</home/Data/PHD1/HuEx-1_0-st-v2.root> in<READ> mode...
>> > > Opening
>> file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>
>> in<READ> mode...
>> > > Opening
>> file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>
>> in<READ> mode...
>> > > Exporting data from tree<UniTest> to
>> file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.txt>...
>> > > Error: UnitID<322394> not found.
>> > > An error has occured: Need to abort current process.
>> > > Error in .local(object, ...) : error in function ‘ExportData’
>> > >
>> > >> class(data.rma)
>> > > [1] "ExprTreeSet"
>> > > attr(,"package")
>> > > [1] "xps"
>> > >> summary(data.rma)
>> > > Length Class Mode
>> > > 1 ExprTreeSet S4
>> > >> sessionInfo()
>> > > R version 2.11.0 (2010-04-22)
>> > > i386-redhat-linux-gnu
>> > >
>> > > locale:
>> > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> > > [9] LC_ADDRESS=C LC_TELEPHONE=C
>> > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> > >
>> > > attached base packages:
>> > > [1] stats graphics grDevices utils datasets methods base
>> > >
>> > > other attached packages:
>> > > [1] xps_1.8.0
>> > >
>> > >
>> > > _________________________________________________________________
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>> > >
>> > >
>> > >
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