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

cstrato cstrato at aon.at
Mon Jun 28 20:34:04 CEST 2010 

Dear John,

In order to get adjusted p-values you need to define the correction 
parameter of "uniTest" first (see ?uniTest for available options), e.g.:
 > unifltr <- 
UniFilter(unitest=c("t.test","two.sided",correction="fdr",0,0.0,FALSE,0.95,TRUE))

Best regards
Christian


On 6/28/10 11:51 AM, John Coulthard wrote:
> Dear Christian
>
> That is working great now, thank you.
>
> One last thing. validData() is reporting the same value for P-Value and
> P-Adjusted.
> Was I supposed to set a flag somewhere to say what kind of adjusted
> P.value I wanted, if so where?
> The P-value I'm getting is un-adjusted, yes?
>
> Thanks for your help
> John
>
>  > rma.ufr <- unifilter(data.rma, filename="tmpdt_TestUnifilter",
> filedir=getwd(), filter=unifltr, group = c("242", "g8", "g8", "g8",
> "242", "242", "g8", "g8", "g8", "242", "242", "242"), verbose = F)
>  > tmp <- validData(rma.ufr)
>  > head(tmp)
> UNIT_ID Statistics Mean1 Mean2 StandardError DegreeOfFreedom
> 2315114 40 -1.86183 25.17190 37.0571 0.299668 10
> 2315132 55 -2.01655 7.70322 11.1137 0.262234 10
> 2315148 60 -3.79757 206.72200 271.8960 0.104111 10
> 2315211 114 2.97650 47.00830 23.9304 0.327255 10
> 2315261 144 -2.04578 43.99160 58.1170 0.196372 10
> 2315306 174 2.07352 577.61600 390.6650 0.272087 10
> P-Value P-Adjusted FoldChange
> 2315114 0.09223710 0.09223710 1.472160
> 2315132 0.07138970 0.07138970 1.442740
> 2315148 0.00349973 0.00349973 1.315280
> 2315211 0.01389060 0.01389060 0.509067
> 2315261 0.06798710 0.06798710 1.321090
> 2315306 0.06489950 0.06489950 0.676341
>
>
>
>  > Date: Wed, 23 Jun 2010 23:45:47 +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,
>  >
>  > 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
>  > >> > >
>  > >> > >
>  > >> > > _________________________________________________________________
>  > >> > > Hotmail: Powerful Free email with security by Microsoft.
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>  > >> > > [[alternative HTML version deleted]]
>  > >> > >
>  > >> > >
>  > >> > >
>  > >> > >
>  > >> > > _______________________________________________
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