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

[cstrato]

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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