xps and unifilter; Error: UnitID not found; error in function ‘ExportData’
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@john-coulthard-3077
Last seen 10.3 years ago
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,FAL SE,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> in <read> mode... Creating new temporary file </home>... Opening file </home> in <read> mode... Unifilter: <32235> genes of <1386572> genes fulfill filter criteria. Opening file </home> in <read> mode... Opening file </home> in <read> mode... Opening file </home> in <read> mode... Exporting data from tree <unitest> to file </home>... 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. [[alternative HTML version deleted]]
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.2 years ago
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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,FAL SE,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> in<read> mode... > Creating new temporary file</home>... > Opening file</home> in<read> mode... > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. > Opening file</home> in<read> mode... > Opening file</home> in<read> mode... > Opening file</home> in<read> mode... > Exporting data from tree<unitest> to file</home>... > 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. > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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,FALS E,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@aon.at > To: bahhab@hotmail.com > CC: bioconductor@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,F ALSE,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> in<read> mode... > > Creating new temporary file</home>... > > Opening file</home> in<read> mode... > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. > > Opening file</home> in<read> mode... > > Opening file</home> in<read> mode... > > Opening file</home> in<read> mode... > > Exporting data from tree<unitest> to file</home>... > > 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. > > > > [[alternative HTML version deleted]] > > > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. [[alternative HTML version deleted]]
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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,TRU E),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,TRU E),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> in<read> mode... > > > Creating new temporary > file</home>... > > > Opening file</home> > in<read> mode... > > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. > > > Opening file</home> in<read> mode... > > > Opening > file</home> > in<read> mode... > > > Opening > file</home> > in<read> mode... > > > Exporting data from tree<unitest> to > file</home>... > > > 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. > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------------------------------------------------- ---- > Hotmail: Powerful Free email with security by Microsoft. Get it now. > <https: signup.live.com="" signup.aspx?id="60969">
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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,TR UE),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,TR UE),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> in<read> mode... >> > > Creating new temporary >> file</home>... >> > > Opening file</home> >> in<read> mode... >> > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. >> > > Opening file</home> in<read> mode... >> > > Opening >> file</home> >> in<read> mode... >> > > Opening >> file</home> >> in<read> mode... >> > > Exporting data from tree<unitest> to >> file</home>... >> > > 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. >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > >> > > >> > > >> > > _______________________________________________ >> > > Bioconductor mailing list >> > > Bioconductor at stat.math.ethz.ch >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> ------------------------------------------------------------------- ----- >> Hotmail: Powerful Free email with security by Microsoft. Get it now. >> <https: signup.live.com="" signup.aspx?id="60969"> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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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@aon.at > To: bahhab@hotmail.com > CC: bioconductor@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@aon.at > >> > To: bahhab@hotmail.com > >> > CC: bioconductor@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> in<read> mode... > >> > > Creating new temporary > >> file</home>... > >> > > Opening file</home> > >> in<read> mode... > >> > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. > >> > > Opening file</home> in<read> mode... > >> > > Opening > >> file</home> > >> in<read> mode... > >> > > Opening > >> file</home> > >> in<read> mode... > >> > > Exporting data from tree<unitest> to > >> file</home>... > >> > > 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. > >> > > > >> > > [[alternative HTML version deleted]] > >> > > > >> > > > >> > > > >> > > > >> > > _______________________________________________ > >> > > Bioconductor mailing list > >> > > Bioconductor@stat.math.ethz.ch > >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > > Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> ----------------------------------------------------------------- ------- > >> Hotmail: Powerful Free email with security by Microsoft. Get it now. > >> <https: signup.live.com="" signup.aspx?id="60969"> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. [[alternative HTML version deleted]]
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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,TRU E),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,TRU E),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> in<read> mode... > > >> > > Creating new temporary > > >> > file</home>... > > >> > > Opening file</home> > > >> in<read> mode... > > >> > > Unifilter:<32235> genes of<1386572> genes fulfill filter criteria. > > >> > > Opening file</home> in<read> mode... > > >> > > Opening > > >> file</home> > > >> in<read> mode... > > >> > > Opening > > >> file</home> > > >> in<read> mode... > > >> > > Exporting data from tree<unitest> to > > >> file</home>... > > >> > > 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. > > >> > > > > >> > > [[alternative HTML version deleted]] > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > _______________________________________________ > > >> > > Bioconductor mailing list > > >> > > Bioconductor at stat.math.ethz.ch > > >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> > > Search the archives: > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > >> > -------------------------------------------------------------------- ---- > > >> Hotmail: Powerful Free email with security by Microsoft. Get it now. > > >> <https: signup.live.com="" signup.aspx?id="60969"> > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------------------------------------------------- ---- > Hotmail: Powerful Free email with security by Microsoft. Get it now. > <https: signup.live.com="" signup.aspx?id="60969">
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