Question: xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
0
gravatar for Dick Beyer
11.6 years ago by
Dick Beyer1.4k
Dick Beyer1.4k wrote:
Hello help, I'm trying out the xps package and have run into an error I can't seem to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. I've successfully created schemes, plotted raw data and so forth, but rma gives me an error: data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", background="pmonly", normalize=TRUE, verbose=TRUE) Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? Since these are Mouse Gene 1.0 ST Arrays, and the default value for exonlevel="", I'm not sure what I'm doing wrong. Here is the details on my DataTreeSet object, data.laspada: str(data.laspada) Formal class 'DataTreeSet' [package "xps"] with 12 slots ..@ bgtreenames: list() ..@ bgrd :'data.frame': 0 obs. of 0 variables ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 slots .. .. ..@ submitter : chr "" .. .. ..@ laboratory : chr "" .. .. ..@ contact : chr "" .. .. ..@ project : list() .. .. ..@ author : list() .. .. ..@ dataset : list() .. .. ..@ source : list() .. .. ..@ sample : list() .. .. ..@ celline : list() .. .. ..@ primarycell : list() .. .. ..@ tissue : list() .. .. ..@ biopsy : list() .. .. ..@ arraytype : list() .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 variables .. .. ..@ treatments :'data.frame': 0 obs. of 0 variables ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with 10 slots .. .. ..@ chipname : chr "MoGene-1_0-st-v1" .. .. ..@ chiptype : chr "GenomeChip" .. .. ..@ probeinfo:List of 8 .. .. .. ..$ nrows : int 1050 .. .. .. ..$ ncols : int 1050 .. .. .. ..$ nprobes : int 906151 .. .. .. ..$ ncontrols : int 6682 .. .. .. ..$ ngenes : int 28815 .. .. .. ..$ nunits : int 35557 .. .. .. ..$ nprobesets: int 35557 .. .. .. ..$ naffx : int 22 .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 -6682 -6682 -6682 -6682 -6682 ... .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 868 454 454 ... .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 454 288 ... .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 ... .. .. ..@ setname : chr "MoGene-1_0-st-v1" .. .. ..@ settype : chr "scheme" .. .. ..@ rootfile : chr "C:/Program Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" .. .. ..@ numtrees : int 5 .. .. ..@ treenames:List of 5 .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" ..@ data :'data.frame': 1102500 obs. of 8 variables: .. ..$ X : int [1:1102500] 0 1 2 3 4 5 6 7 8 9 ... .. ..$ Y : int [1:1102500] 0 0 0 0 0 0 0 0 0 0 ... .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 69 4873 104 35 87 5308 83 4819 60 ... .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 49 3194 47 35 37 3339 50 3300 71 ... .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 66 4482 49 41 60 5037 60 5038 51 ... .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 50 3298 42 33 69 3610 51 3972 83 ... .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 74 5054 66 41 50 5679 72 5810 65 ... .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 62 4131 50 28 49 4824 80 4647 57 ... ..@ params : list() ..@ setname : chr "DataSet" ..@ settype : chr "rawdata" ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc xps/laspadaCMRap_cel.root" ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" ..@ numtrees : num 6 ..@ treenames :List of 6 .. ..$ : chr "Albert LaSpada CM3 07May08.cel" .. ..$ : chr "Albert LaSpada CM4 07May08.cel" .. ..$ : chr "Albert LaSpada CM5 07May08.cel" .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" And my sessionInfo is: sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xps_1.0.0 I also am using ROOT from root_v5.18.00.win32.tar.gz. Any help or suggestions would be greatly appreciated. Thanks, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** *********
chipname affy xps • 711 views
ADD COMMENTlink modified 11.6 years ago by cstrato3.9k • written 11.6 years ago by Dick Beyer1.4k
Answer: xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
0
gravatar for cstrato
11.6 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:
Dear Dirk Please not that function rma is common to Expression, Genome and Exon arrays, this I decided to use default settings for Expression arrays, since these are still most common. If you look at the help file for rma you will see the following Details: Following exonlevel annotations are valid for whole genome arrays: core: probesets with category ?unique? and ?mixed?. metacore: probesets with category ?unique? only. affx: standard AFFX controls. all: combination of above. Thus you need to use e.g. exonlevel="affx+core" I hope that this information can help you solve your problem. Best regards Christian _._._._._._._._._._._._._._._._ C.h.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 _._._._._._._._._._._._._._._._ Dick Beyer wrote: > Hello help, > > I'm trying out the xps package and have run into an error I can't seem > to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. > > I've successfully created schemes, plotted raw data and so forth, but > rma gives me an error: > > data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", > background="pmonly", normalize=TRUE, verbose=TRUE) > > Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? > > Since these are Mouse Gene 1.0 ST Arrays, and the default value for > exonlevel="", I'm not sure what I'm doing wrong. > > Here is the details on my DataTreeSet object, data.laspada: > > str(data.laspada) > Formal class 'DataTreeSet' [package "xps"] with 12 slots > ..@ bgtreenames: list() > ..@ bgrd :'data.frame': 0 obs. of 0 variables > ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 > slots > .. .. ..@ submitter : chr "" > .. .. ..@ laboratory : chr "" > .. .. ..@ contact : chr "" > .. .. ..@ project : list() > .. .. ..@ author : list() > .. .. ..@ dataset : list() > .. .. ..@ source : list() > .. .. ..@ sample : list() > .. .. ..@ celline : list() > .. .. ..@ primarycell : list() > .. .. ..@ tissue : list() > .. .. ..@ biopsy : list() > .. .. ..@ arraytype : list() > .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 variables > .. .. ..@ treatments :'data.frame': 0 obs. of 0 variables > ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with 10 > slots > .. .. ..@ chipname : chr "MoGene-1_0-st-v1" > .. .. ..@ chiptype : chr "GenomeChip" > .. .. ..@ probeinfo:List of 8 > .. .. .. ..$ nrows : int 1050 > .. .. .. ..$ ncols : int 1050 > .. .. .. ..$ nprobes : int 906151 > .. .. .. ..$ ncontrols : int 6682 > .. .. .. ..$ ngenes : int 28815 > .. .. .. ..$ nunits : int 35557 > .. .. .. ..$ nprobesets: int 35557 > .. .. .. ..$ naffx : int 22 > .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: > .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 > -6682 -6682 -6682 -6682 -6682 ... > .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 868 > 454 454 ... > .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 > 454 288 ... > .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 -16 > -16 -16 ... > .. .. ..@ setname : chr "MoGene-1_0-st-v1" > .. .. ..@ settype : chr "scheme" > .. .. ..@ rootfile : chr "C:/Program > Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" > .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" > .. .. ..@ numtrees : int 5 > .. .. ..@ treenames:List of 5 > .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" > .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" > .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" > .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" > .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" > ..@ data :'data.frame': 1102500 obs. of 8 variables: > .. ..$ X : int [1:1102500] 0 1 2 3 > 4 5 6 7 8 9 ... > .. ..$ Y : int [1:1102500] 0 0 0 0 > 0 0 0 0 0 0 ... > .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 69 > 4873 104 35 87 5308 83 4819 60 ... > .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 49 > 3194 47 35 37 3339 50 3300 71 ... > .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 66 > 4482 49 41 60 5037 60 5038 51 ... > .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 50 > 3298 42 33 69 3610 51 3972 83 ... > .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 74 > 5054 66 41 50 5679 72 5810 65 ... > .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 62 > 4131 50 28 49 4824 80 4647 57 ... > ..@ params : list() > ..@ setname : chr "DataSet" > ..@ settype : chr "rawdata" > ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc > xps/laspadaCMRap_cel.root" > ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" > ..@ numtrees : num 6 > ..@ treenames :List of 6 > .. ..$ : chr "Albert LaSpada CM3 07May08.cel" > .. ..$ : chr "Albert LaSpada CM4 07May08.cel" > .. ..$ : chr "Albert LaSpada CM5 07May08.cel" > .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" > .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" > .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" > > And my sessionInfo is: > sessionInfo() > R version 2.7.0 (2008-04-22) i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.0.0 > > I also am using ROOT from root_v5.18.00.win32.tar.gz. > > Any help or suggestions would be greatly appreciated. > > Thanks, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > _______________________________________________ > 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 > >
ADD COMMENTlink written 11.6 years ago by cstrato3.9k
Hi Christian, Thanks for pointing this out. I tried several of the combinations listed in the documentation for rma. However, I now get a different error message: > data.rma1 <- rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="core") Error in .local(object, ...) : error in function ?PreprocessRMA? > data.rma2 <- rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="metacore") Error in .local(object, ...) : error in function ?PreprocessRMA? > data.rma3 <- rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="affx") Error in .local(object, ...) : error in function ?PreprocessRMA? > data.rma4 <- rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="affx+core") Error in .local(object, ...) : error in function ?PreprocessRMA? > data.rma5 <- rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="all") Error in .local(object, ...) : error in function ?PreprocessRMA? > data.rma6 <- rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",backgroun d="pmonly",normalize=TRUE, verbose=TRUE,exonlevel="") Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? Would you please suggest what I could do next? Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 9 May 2008, cstrato wrote: > Dear Dirk > > Please not that function rma is common to Expression, Genome and Exon arrays, > this I decided to use default settings for Expression arrays, since these are > still most common. > > If you look at the help file for rma you will see the following Details: > Following exonlevel annotations are valid for whole genome arrays: > core: probesets with category ?unique? and ?mixed?. > metacore: probesets with category ?unique? only. > affx: standard AFFX controls. > all: combination of above. > > Thus you need to use e.g. exonlevel="affx+core" > > I hope that this information can help you solve your problem. > > Best regards > Christian > _._._._._._._._._._._._._._._._ > C.h.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 > _._._._._._._._._._._._._._._._ > > Dick Beyer wrote: >> Hello help, >> >> I'm trying out the xps package and have run into an error I can't seem to >> workaround for affy Mouse ST MoGene-1_0-st-v1 array data. >> >> I've successfully created schemes, plotted raw data and so forth, but rma >> gives me an error: >> >> data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", >> background="pmonly", normalize=TRUE, verbose=TRUE) >> >> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >> >> Since these are Mouse Gene 1.0 ST Arrays, and the default value for >> exonlevel="", I'm not sure what I'm doing wrong. >> >> Here is the details on my DataTreeSet object, data.laspada: >> >> str(data.laspada) >> Formal class 'DataTreeSet' [package "xps"] with 12 slots >> ..@ bgtreenames: list() >> ..@ bgrd :'data.frame': 0 obs. of 0 variables >> ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 slots >> .. .. ..@ submitter : chr "" >> .. .. ..@ laboratory : chr "" >> .. .. ..@ contact : chr "" >> .. .. ..@ project : list() >> .. .. ..@ author : list() >> .. .. ..@ dataset : list() >> .. .. ..@ source : list() >> .. .. ..@ sample : list() >> .. .. ..@ celline : list() >> .. .. ..@ primarycell : list() >> .. .. ..@ tissue : list() >> .. .. ..@ biopsy : list() >> .. .. ..@ arraytype : list() >> .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 variables >> .. .. ..@ treatments :'data.frame': 0 obs. of 0 variables >> ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with 10 slots >> .. .. ..@ chipname : chr "MoGene-1_0-st-v1" >> .. .. ..@ chiptype : chr "GenomeChip" >> .. .. ..@ probeinfo:List of 8 >> .. .. .. ..$ nrows : int 1050 >> .. .. .. ..$ ncols : int 1050 >> .. .. .. ..$ nprobes : int 906151 >> .. .. .. ..$ ncontrols : int 6682 >> .. .. .. ..$ ngenes : int 28815 >> .. .. .. ..$ nunits : int 35557 >> .. .. .. ..$ nprobesets: int 35557 >> .. .. .. ..$ naffx : int 22 >> .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: >> .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 -6682 >> -6682 -6682 -6682 -6682 ... >> .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 868 454 >> 454 ... >> .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 454 288 >> ... >> .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 -16 -16 >> -16 ... >> .. .. ..@ setname : chr "MoGene-1_0-st-v1" >> .. .. ..@ settype : chr "scheme" >> .. .. ..@ rootfile : chr "C:/Program >> Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" >> .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" >> .. .. ..@ numtrees : int 5 >> .. .. ..@ treenames:List of 5 >> .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" >> .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" >> .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" >> .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" >> .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" >> ..@ data :'data.frame': 1102500 obs. of 8 variables: >> .. ..$ X : int [1:1102500] 0 1 2 3 4 5 6 >> 7 8 9 ... >> .. ..$ Y : int [1:1102500] 0 0 0 0 0 0 0 >> 0 0 0 ... >> .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 69 4873 >> 104 35 87 5308 83 4819 60 ... >> .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 49 3194 >> 47 35 37 3339 50 3300 71 ... >> .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 66 4482 >> 49 41 60 5037 60 5038 51 ... >> .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 50 3298 >> 42 33 69 3610 51 3972 83 ... >> .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 74 5054 >> 66 41 50 5679 72 5810 65 ... >> .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 62 4131 >> 50 28 49 4824 80 4647 57 ... >> ..@ params : list() >> ..@ setname : chr "DataSet" >> ..@ settype : chr "rawdata" >> ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc >> xps/laspadaCMRap_cel.root" >> ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" >> ..@ numtrees : num 6 >> ..@ treenames :List of 6 >> .. ..$ : chr "Albert LaSpada CM3 07May08.cel" >> .. ..$ : chr "Albert LaSpada CM4 07May08.cel" >> .. ..$ : chr "Albert LaSpada CM5 07May08.cel" >> .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" >> .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" >> .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" >> >> And my sessionInfo is: >> sessionInfo() >> R version 2.7.0 (2008-04-22) i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xps_1.0.0 >> >> I also am using ROOT from root_v5.18.00.win32.tar.gz. >> >> Any help or suggestions would be greatly appreciated. >> >> Thanks, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ******************************************************************* ************ >> _______________________________________________ >> 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 >> >> > >
ADD REPLYlink written 11.6 years ago by Dick Beyer1.4k
Dear Dick Thank you for your tests, which make it clear to me that I need to improve the help files. Since MoGene arrays as well as exon arrays have no MM, you need to set: background="antigenomic" Please have a look at directory "xps/examples" which contains files "script4xps.R" and "script4exon.R": In these scripts I give numerous examples which you can copy/paste and adapt to your needs, especially I describe how to use the Affymetrix human tissue dataset with arrays HG-U133_Plus_2, HuGene-1_0-st-v1.r3 and HuEx-1_0-st-v2.r2. For HuGene the rma example is as follows: data.rma <- rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", background="antigenomic",normalize=T,exonlevel="metacore+affx") Please let me know if these informations could help you solve your problem. Best regards Christian Dick Beyer wrote: > Hi Christian, > > Thanks for pointing this out. I tried several of the combinations > listed in the documentation for rma. However, I now get a different > error message: > >> data.rma1 <- >> rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="core") > Error in .local(object, ...) : error in function ?PreprocessRMA? >> data.rma2 <- >> rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="metacore") > Error in .local(object, ...) : error in function ?PreprocessRMA? >> data.rma3 <- >> rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="affx") > Error in .local(object, ...) : error in function ?PreprocessRMA? >> data.rma4 <- >> rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="affx+core") > Error in .local(object, ...) : error in function ?PreprocessRMA? >> data.rma5 <- >> rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="all") > Error in .local(object, ...) : error in function ?PreprocessRMA? >> data.rma6 <- >> rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",background="pmonly",n ormalize=TRUE, >> verbose=TRUE,exonlevel="") > Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? > > Would you please suggest what I could do next? > Thanks very much, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > On Fri, 9 May 2008, cstrato wrote: > >> Dear Dirk >> >> Please not that function rma is common to Expression, Genome and Exon >> arrays, this I decided to use default settings for Expression arrays, >> since these are still most common. >> >> If you look at the help file for rma you will see the following Details: >> Following exonlevel annotations are valid for whole genome arrays: >> core: probesets with category ?unique? and ?mixed?. >> metacore: probesets with category ?unique? only. >> affx: standard AFFX controls. >> all: combination of above. >> >> Thus you need to use e.g. exonlevel="affx+core" >> >> I hope that this information can help you solve your problem. >> >> Best regards >> Christian >> _._._._._._._._._._._._._._._._ >> C.h.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 >> _._._._._._._._._._._._._._._._ >> >> Dick Beyer wrote: >>> Hello help, >>> >>> I'm trying out the xps package and have run into an error I can't >>> seem to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. >>> >>> I've successfully created schemes, plotted raw data and so forth, >>> but rma gives me an error: >>> >>> data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", >>> background="pmonly", normalize=TRUE, verbose=TRUE) >>> >>> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >>> >>> Since these are Mouse Gene 1.0 ST Arrays, and the default value for >>> exonlevel="", I'm not sure what I'm doing wrong. >>> >>> Here is the details on my DataTreeSet object, data.laspada: >>> >>> str(data.laspada) >>> Formal class 'DataTreeSet' [package "xps"] with 12 slots >>> ..@ bgtreenames: list() >>> ..@ bgrd :'data.frame': 0 obs. of 0 variables >>> ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 >>> slots >>> .. .. ..@ submitter : chr "" >>> .. .. ..@ laboratory : chr "" >>> .. .. ..@ contact : chr "" >>> .. .. ..@ project : list() >>> .. .. ..@ author : list() >>> .. .. ..@ dataset : list() >>> .. .. ..@ source : list() >>> .. .. ..@ sample : list() >>> .. .. ..@ celline : list() >>> .. .. ..@ primarycell : list() >>> .. .. ..@ tissue : list() >>> .. .. ..@ biopsy : list() >>> .. .. ..@ arraytype : list() >>> .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 variables >>> .. .. ..@ treatments :'data.frame': 0 obs. of 0 variables >>> ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with >>> 10 slots >>> .. .. ..@ chipname : chr "MoGene-1_0-st-v1" >>> .. .. ..@ chiptype : chr "GenomeChip" >>> .. .. ..@ probeinfo:List of 8 >>> .. .. .. ..$ nrows : int 1050 >>> .. .. .. ..$ ncols : int 1050 >>> .. .. .. ..$ nprobes : int 906151 >>> .. .. .. ..$ ncontrols : int 6682 >>> .. .. .. ..$ ngenes : int 28815 >>> .. .. .. ..$ nunits : int 35557 >>> .. .. .. ..$ nprobesets: int 35557 >>> .. .. .. ..$ naffx : int 22 >>> .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: >>> .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 >>> -6682 -6682 -6682 -6682 -6682 ... >>> .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 >>> 868 454 454 ... >>> .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 >>> 454 288 ... >>> .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 >>> -16 -16 -16 ... >>> .. .. ..@ setname : chr "MoGene-1_0-st-v1" >>> .. .. ..@ settype : chr "scheme" >>> .. .. ..@ rootfile : chr "C:/Program >>> Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" >>> .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" >>> .. .. ..@ numtrees : int 5 >>> .. .. ..@ treenames:List of 5 >>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" >>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" >>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" >>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" >>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" >>> ..@ data :'data.frame': 1102500 obs. of 8 variables: >>> .. ..$ X : int [1:1102500] 0 1 2 >>> 3 4 5 6 7 8 9 ... >>> .. ..$ Y : int [1:1102500] 0 0 0 >>> 0 0 0 0 0 0 0 ... >>> .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 >>> 69 4873 104 35 87 5308 83 4819 60 ... >>> .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 >>> 49 3194 47 35 37 3339 50 3300 71 ... >>> .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 >>> 66 4482 49 41 60 5037 60 5038 51 ... >>> .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 >>> 50 3298 42 33 69 3610 51 3972 83 ... >>> .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 >>> 74 5054 66 41 50 5679 72 5810 65 ... >>> .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 >>> 62 4131 50 28 49 4824 80 4647 57 ... >>> ..@ params : list() >>> ..@ setname : chr "DataSet" >>> ..@ settype : chr "rawdata" >>> ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc >>> xps/laspadaCMRap_cel.root" >>> ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" >>> ..@ numtrees : num 6 >>> ..@ treenames :List of 6 >>> .. ..$ : chr "Albert LaSpada CM3 07May08.cel" >>> .. ..$ : chr "Albert LaSpada CM4 07May08.cel" >>> .. ..$ : chr "Albert LaSpada CM5 07May08.cel" >>> .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" >>> .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" >>> .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" >>> >>> And my sessionInfo is: >>> sessionInfo() >>> R version 2.7.0 (2008-04-22) i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] xps_1.0.0 >>> >>> I also am using ROOT from root_v5.18.00.win32.tar.gz. >>> >>> Any help or suggestions would be greatly appreciated. >>> >>> Thanks, >>> Dick >>> ****************************************************************** ************* >>> Richard P. Beyer, Ph.D. University of Washington >>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>> Seattle, WA 98105-6099 >>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>> http://staff.washington.edu/~dbeyer >>> ****************************************************************** ************* >>> _______________________________________________ >>> 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 >>> >>> >> >> > > > >
ADD REPLYlink written 11.6 years ago by cstrato3.9k
Hi Christian, Thanks for your good help. I'm a repeat offender when it comes to not reading all the way through examples. Thanks for your patience. Using background="antigenomic" made my rma call work just fine. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 9 May 2008, cstrato wrote: > Dear Dick > > Thank you for your tests, which make it clear to me that I need to improve the > help files. > > Since MoGene arrays as well as exon arrays have no MM, you need to set: > background="antigenomic" > > Please have a look at directory "xps/examples" which contains files > "script4xps.R" and "script4exon.R": > In these scripts I give numerous examples which you can copy/paste and adapt to > your needs, especially I describe how to use the Affymetrix human tissue > dataset with arrays HG-U133_Plus_2, HuGene-1_0-st-v1.r3 and HuEx- 1_0-st-v2.r2. > > For HuGene the rma example is as follows: > data.rma <- rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", > background="antigenomic",normalize=T,exonlevel="metacore+affx") > > Please let me know if these informations could help you solve your problem. > > Best regards > Christian > > > Dick Beyer wrote: >> Hi Christian, >> >> Thanks for pointing this out. I tried several of the combinations listed in >> the documentation for rma. However, I now get a different error message: >> >>> data.rma1 <- >>> rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="core") >> Error in .local(object, ...) : error in function ?PreprocessRMA? >>> data.rma2 <- >>> rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="metacore") >> Error in .local(object, ...) : error in function ?PreprocessRMA? >>> data.rma3 <- >>> rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="affx") >> Error in .local(object, ...) : error in function ?PreprocessRMA? >>> data.rma4 <- >>> rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="affx+core") >> Error in .local(object, ...) : error in function ?PreprocessRMA? >>> data.rma5 <- >>> rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="all") >> Error in .local(object, ...) : error in function ?PreprocessRMA? >>> data.rma6 <- >>> rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",background="pmonly", normalize=TRUE, >>> verbose=TRUE,exonlevel="") >> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >> >> Would you please suggest what I could do next? >> Thanks very much, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ******************************************************************* ************ >> On Fri, 9 May 2008, cstrato wrote: >> >>> Dear Dirk >>> >>> Please not that function rma is common to Expression, Genome and Exon >>> arrays, this I decided to use default settings for Expression arrays, >>> since these are still most common. >>> >>> If you look at the help file for rma you will see the following Details: >>> Following exonlevel annotations are valid for whole genome arrays: >>> core: probesets with category ?unique? and ?mixed?. >>> metacore: probesets with category ?unique? only. >>> affx: standard AFFX controls. >>> all: combination of above. >>> >>> Thus you need to use e.g. exonlevel="affx+core" >>> >>> I hope that this information can help you solve your problem. >>> >>> Best regards >>> Christian >>> _._._._._._._._._._._._._._._._ >>> C.h.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 >>> _._._._._._._._._._._._._._._._ >>> >>> Dick Beyer wrote: >>>> Hello help, >>>> >>>> I'm trying out the xps package and have run into an error I can't seem >>>> to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. >>>> >>>> I've successfully created schemes, plotted raw data and so forth, but >>>> rma gives me an error: >>>> >>>> data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", >>>> background="pmonly", normalize=TRUE, verbose=TRUE) >>>> >>>> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >>>> >>>> Since these are Mouse Gene 1.0 ST Arrays, and the default value for >>>> exonlevel="", I'm not sure what I'm doing wrong. >>>> >>>> Here is the details on my DataTreeSet object, data.laspada: >>>> >>>> str(data.laspada) >>>> Formal class 'DataTreeSet' [package "xps"] with 12 slots >>>> ..@ bgtreenames: list() >>>> ..@ bgrd :'data.frame': 0 obs. of 0 variables >>>> ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 >>>> slots >>>> .. .. ..@ submitter : chr "" >>>> .. .. ..@ laboratory : chr "" >>>> .. .. ..@ contact : chr "" >>>> .. .. ..@ project : list() >>>> .. .. ..@ author : list() >>>> .. .. ..@ dataset : list() >>>> .. .. ..@ source : list() >>>> .. .. ..@ sample : list() >>>> .. .. ..@ celline : list() >>>> .. .. ..@ primarycell : list() >>>> .. .. ..@ tissue : list() >>>> .. .. ..@ biopsy : list() >>>> .. .. ..@ arraytype : list() >>>> .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 variables >>>> .. .. ..@ treatments :'data.frame': 0 obs. of 0 variables >>>> ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with 10 >>>> slots >>>> .. .. ..@ chipname : chr "MoGene-1_0-st-v1" >>>> .. .. ..@ chiptype : chr "GenomeChip" >>>> .. .. ..@ probeinfo:List of 8 >>>> .. .. .. ..$ nrows : int 1050 >>>> .. .. .. ..$ ncols : int 1050 >>>> .. .. .. ..$ nprobes : int 906151 >>>> .. .. .. ..$ ncontrols : int 6682 >>>> .. .. .. ..$ ngenes : int 28815 >>>> .. .. .. ..$ nunits : int 35557 >>>> .. .. .. ..$ nprobesets: int 35557 >>>> .. .. .. ..$ naffx : int 22 >>>> .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: >>>> .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 >>>> -6682 -6682 -6682 -6682 -6682 ... >>>> .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 868 >>>> 454 454 ... >>>> .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 454 >>>> 288 ... >>>> .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 -16 >>>> -16 -16 ... >>>> .. .. ..@ setname : chr "MoGene-1_0-st-v1" >>>> .. .. ..@ settype : chr "scheme" >>>> .. .. ..@ rootfile : chr "C:/Program >>>> Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" >>>> .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" >>>> .. .. ..@ numtrees : int 5 >>>> .. .. ..@ treenames:List of 5 >>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" >>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" >>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" >>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" >>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" >>>> ..@ data :'data.frame': 1102500 obs. of 8 variables: >>>> .. ..$ X : int [1:1102500] 0 1 2 3 4 >>>> 5 6 7 8 9 ... >>>> .. ..$ Y : int [1:1102500] 0 0 0 0 0 >>>> 0 0 0 0 0 ... >>>> .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 69 >>>> 4873 104 35 87 5308 83 4819 60 ... >>>> .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 49 >>>> 3194 47 35 37 3339 50 3300 71 ... >>>> .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 66 >>>> 4482 49 41 60 5037 60 5038 51 ... >>>> .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 50 >>>> 3298 42 33 69 3610 51 3972 83 ... >>>> .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 74 >>>> 5054 66 41 50 5679 72 5810 65 ... >>>> .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 62 >>>> 4131 50 28 49 4824 80 4647 57 ... >>>> ..@ params : list() >>>> ..@ setname : chr "DataSet" >>>> ..@ settype : chr "rawdata" >>>> ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc >>>> xps/laspadaCMRap_cel.root" >>>> ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" >>>> ..@ numtrees : num 6 >>>> ..@ treenames :List of 6 >>>> .. ..$ : chr "Albert LaSpada CM3 07May08.cel" >>>> .. ..$ : chr "Albert LaSpada CM4 07May08.cel" >>>> .. ..$ : chr "Albert LaSpada CM5 07May08.cel" >>>> .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" >>>> .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" >>>> .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" >>>> >>>> And my sessionInfo is: >>>> sessionInfo() >>>> R version 2.7.0 (2008-04-22) i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>> States.1252;LC_MONETARY=English_United >>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] xps_1.0.0 >>>> >>>> I also am using ROOT from root_v5.18.00.win32.tar.gz. >>>> >>>> Any help or suggestions would be greatly appreciated. >>>> >>>> Thanks, >>>> Dick >>>> ***************************************************************** ************** >>>> Richard P. Beyer, Ph.D. University of Washington >>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>> Seattle, WA 98105-6099 >>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>> http://staff.washington.edu/~dbeyer >>>> ***************************************************************** ************** >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> >>> >> >> >> >> > >
ADD REPLYlink written 11.6 years ago by Dick Beyer1.4k
Dear Dick I am glad to hear that you could now run rma. Please feel free to inform me about any potential problems, omissions in the help file, or potential improvements. Best regards Christian Dick Beyer wrote: > Hi Christian, > > Thanks for your good help. I'm a repeat offender when it comes to not > reading all the way through examples. Thanks for your patience. > > Using background="antigenomic" made my rma call work just fine. > > Cheers, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > On Fri, 9 May 2008, cstrato wrote: > >> Dear Dick >> >> Thank you for your tests, which make it clear to me that I need to >> improve the help files. >> >> Since MoGene arrays as well as exon arrays have no MM, you need to >> set: background="antigenomic" >> >> Please have a look at directory "xps/examples" which contains files >> "script4xps.R" and "script4exon.R": >> In these scripts I give numerous examples which you can copy/paste >> and adapt to your needs, especially I describe how to use the >> Affymetrix human tissue dataset with arrays HG-U133_Plus_2, >> HuGene-1_0-st-v1.r3 and HuEx-1_0-st-v2.r2. >> >> For HuGene the rma example is as follows: >> data.rma <- >> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", >> >> background="antigenomic",normalize=T,exonlevel="metacore+affx") >> >> Please let me know if these informations could help you solve your >> problem. >> >> Best regards >> Christian >> >> >> Dick Beyer wrote: >>> Hi Christian, >>> >>> Thanks for pointing this out. I tried several of the combinations >>> listed in the documentation for rma. However, I now get a different >>> error message: >>> >>>> data.rma1 <- >>>> rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="core") >>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>> data.rma2 <- >>>> rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="metacore") >>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>> data.rma3 <- >>>> rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="affx") >>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>> data.rma4 <- >>>> rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="affx+core") >>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>> data.rma5 <- >>>> rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="all") >>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>> data.rma6 <- >>>> rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",background="pmonly" ,normalize=TRUE, >>>> verbose=TRUE,exonlevel="") >>> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >>> >>> Would you please suggest what I could do next? >>> Thanks very much, >>> Dick >>> ****************************************************************** ************* >>> Richard P. Beyer, Ph.D. University of Washington >>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>> Seattle, WA 98105-6099 >>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>> http://staff.washington.edu/~dbeyer >>> ****************************************************************** ************* >>> On Fri, 9 May 2008, cstrato wrote: >>> >>>> Dear Dirk >>>> >>>> Please not that function rma is common to Expression, Genome and >>>> Exon arrays, this I decided to use default settings for Expression >>>> arrays, since these are still most common. >>>> >>>> If you look at the help file for rma you will see the following >>>> Details: >>>> Following exonlevel annotations are valid for whole genome arrays: >>>> core: probesets with category ?unique? and ?mixed?. >>>> metacore: probesets with category ?unique? only. >>>> affx: standard AFFX controls. >>>> all: combination of above. >>>> >>>> Thus you need to use e.g. exonlevel="affx+core" >>>> >>>> I hope that this information can help you solve your problem. >>>> >>>> Best regards >>>> Christian >>>> _._._._._._._._._._._._._._._._ >>>> C.h.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 >>>> _._._._._._._._._._._._._._._._ >>>> >>>> Dick Beyer wrote: >>>>> Hello help, >>>>> >>>>> I'm trying out the xps package and have run into an error I can't >>>>> seem to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. >>>>> >>>>> I've successfully created schemes, plotted raw data and so forth, >>>>> but rma gives me an error: >>>>> >>>>> data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", >>>>> background="pmonly", normalize=TRUE, verbose=TRUE) >>>>> >>>>> Error in exonLevel(exonlevel, chiptype) : invalid argument >>>>> ?exonlevel? >>>>> >>>>> Since these are Mouse Gene 1.0 ST Arrays, and the default value >>>>> for exonlevel="", I'm not sure what I'm doing wrong. >>>>> >>>>> Here is the details on my DataTreeSet object, data.laspada: >>>>> >>>>> str(data.laspada) >>>>> Formal class 'DataTreeSet' [package "xps"] with 12 slots >>>>> ..@ bgtreenames: list() >>>>> ..@ bgrd :'data.frame': 0 obs. of 0 variables >>>>> ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with >>>>> 15 slots >>>>> .. .. ..@ submitter : chr "" >>>>> .. .. ..@ laboratory : chr "" >>>>> .. .. ..@ contact : chr "" >>>>> .. .. ..@ project : list() >>>>> .. .. ..@ author : list() >>>>> .. .. ..@ dataset : list() >>>>> .. .. ..@ source : list() >>>>> .. .. ..@ sample : list() >>>>> .. .. ..@ celline : list() >>>>> .. .. ..@ primarycell : list() >>>>> .. .. ..@ tissue : list() >>>>> .. .. ..@ biopsy : list() >>>>> .. .. ..@ arraytype : list() >>>>> .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 >>>>> variables >>>>> .. .. ..@ treatments :'data.frame': 0 obs. of 0 >>>>> variables >>>>> ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] >>>>> with 10 slots >>>>> .. .. ..@ chipname : chr "MoGene-1_0-st-v1" >>>>> .. .. ..@ chiptype : chr "GenomeChip" >>>>> .. .. ..@ probeinfo:List of 8 >>>>> .. .. .. ..$ nrows : int 1050 >>>>> .. .. .. ..$ ncols : int 1050 >>>>> .. .. .. ..$ nprobes : int 906151 >>>>> .. .. .. ..$ ncontrols : int 6682 >>>>> .. .. .. ..$ ngenes : int 28815 >>>>> .. .. .. ..$ nunits : int 35557 >>>>> .. .. .. ..$ nprobesets: int 35557 >>>>> .. .. .. ..$ naffx : int 22 >>>>> .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: >>>>> .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 >>>>> -6682 -6682 -6682 -6682 -6682 -6682 ... >>>>> .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 >>>>> 868 454 454 ... >>>>> .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 >>>>> 24 454 288 ... >>>>> .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 >>>>> -16 -16 -16 ... >>>>> .. .. ..@ setname : chr "MoGene-1_0-st-v1" >>>>> .. .. ..@ settype : chr "scheme" >>>>> .. .. ..@ rootfile : chr "C:/Program >>>>> Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" >>>>> .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" >>>>> .. .. ..@ numtrees : int 5 >>>>> .. .. ..@ treenames:List of 5 >>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" >>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" >>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" >>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" >>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" >>>>> ..@ data :'data.frame': 1102500 obs. of 8 variables: >>>>> .. ..$ X : int [1:1102500] 0 1 >>>>> 2 3 4 5 6 7 8 9 ... >>>>> .. ..$ Y : int [1:1102500] 0 0 >>>>> 0 0 0 0 0 0 0 0 ... >>>>> .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] >>>>> 4657 69 4873 104 35 87 5308 83 4819 60 ... >>>>> .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] >>>>> 2986 49 3194 47 35 37 3339 50 3300 71 ... >>>>> .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] >>>>> 4393 66 4482 49 41 60 5037 60 5038 51 ... >>>>> .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] >>>>> 2966 50 3298 42 33 69 3610 51 3972 83 ... >>>>> .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] >>>>> 4872 74 5054 66 41 50 5679 72 5810 65 ... >>>>> .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] >>>>> 4278 62 4131 50 28 49 4824 80 4647 57 ... >>>>> ..@ params : list() >>>>> ..@ setname : chr "DataSet" >>>>> ..@ settype : chr "rawdata" >>>>> ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc >>>>> xps/laspadaCMRap_cel.root" >>>>> ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" >>>>> ..@ numtrees : num 6 >>>>> ..@ treenames :List of 6 >>>>> .. ..$ : chr "Albert LaSpada CM3 07May08.cel" >>>>> .. ..$ : chr "Albert LaSpada CM4 07May08.cel" >>>>> .. ..$ : chr "Albert LaSpada CM5 07May08.cel" >>>>> .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" >>>>> .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" >>>>> .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" >>>>> >>>>> And my sessionInfo is: >>>>> sessionInfo() >>>>> R version 2.7.0 (2008-04-22) i386-pc-mingw32 >>>>> >>>>> locale: >>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>>> States.1252;LC_MONETARY=English_United >>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] xps_1.0.0 >>>>> >>>>> I also am using ROOT from root_v5.18.00.win32.tar.gz. >>>>> >>>>> Any help or suggestions would be greatly appreciated. >>>>> >>>>> Thanks, >>>>> Dick >>>>> **************************************************************** *************** >>>>> Richard P. Beyer, Ph.D. University of Washington >>>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>>> Seattle, WA 98105-6099 >>>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>>> http://staff.washington.edu/~dbeyer >>>>> **************************************************************** *************** >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> >> >> > > > >
ADD REPLYlink written 11.6 years ago by cstrato3.9k
Hi Christian, Is there a choice of values to the agruments for rma that gets the same results as Affy Expression Console? I notice that from Affy Expression Console I get an output with 35557 rows, but with either of these choices: data.rma7 <- rma(data.laspada, "laspadaCMRapRMA7",tmpdir="",background="antigenomic",normalize=TRUE, verbose=TRUE,exonlevel="affx+core") data.rma8 <- rma(data.laspada, "laspadaCMRapRMA8",tmpdir="",background="antigenomic",normalize=TRUE, verbose=TRUE,exonlevel="all") then validData(data.rma7) or validData(data.rma8) gives me a matrix with just 28837 rows. Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 9 May 2008, cstrato wrote: > Dear Dick > > I am glad to hear that you could now run rma. > > Please feel free to inform me about any potential problems, omissions in the > help file, or potential improvements. > > Best regards > Christian > > > Dick Beyer wrote: >> Hi Christian, >> >> Thanks for your good help. I'm a repeat offender when it comes to not >> reading all the way through examples. Thanks for your patience. >> >> Using background="antigenomic" made my rma call work just fine. >> >> Cheers, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ******************************************************************* ************ >> On Fri, 9 May 2008, cstrato wrote: >> >>> Dear Dick >>> >>> Thank you for your tests, which make it clear to me that I need to improve >>> the help files. >>> >>> Since MoGene arrays as well as exon arrays have no MM, you need to set: >>> background="antigenomic" >>> >>> Please have a look at directory "xps/examples" which contains files >>> "script4xps.R" and "script4exon.R": >>> In these scripts I give numerous examples which you can copy/paste and >>> adapt to your needs, especially I describe how to use the Affymetrix human >>> tissue dataset with arrays HG-U133_Plus_2, HuGene-1_0-st-v1.r3 and >>> HuEx-1_0-st-v2.r2. >>> >>> For HuGene the rma example is as follows: >>> data.rma <- >>> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", >>> background="antigenomic",normalize=T,exonlevel="metacore+affx") >>> >>> Please let me know if these informations could help you solve your >>> problem. >>> >>> Best regards >>> Christian >>> >>> >>> Dick Beyer wrote: >>>> Hi Christian, >>>> >>>> Thanks for pointing this out. I tried several of the combinations >>>> listed in the documentation for rma. However, I now get a different >>>> error message: >>>> >>>>> data.rma1 <- >>>>> rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="core") >>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>> data.rma2 <- >>>>> rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="metacore") >>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>> data.rma3 <- >>>>> rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="affx") >>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>> data.rma4 <- >>>>> rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="affx+core") >>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>> data.rma5 <- >>>>> rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="all") >>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>> data.rma6 <- >>>>> rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",background="pmonly ",normalize=TRUE, >>>>> verbose=TRUE,exonlevel="") >>>> Error in exonLevel(exonlevel, chiptype) : invalid argument ?exonlevel? >>>> >>>> Would you please suggest what I could do next? >>>> Thanks very much, >>>> Dick >>>> ***************************************************************** ************** >>>> Richard P. Beyer, Ph.D. University of Washington >>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>> Seattle, WA 98105-6099 >>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>> http://staff.washington.edu/~dbeyer >>>> ***************************************************************** ************** >>>> On Fri, 9 May 2008, cstrato wrote: >>>> >>>>> Dear Dirk >>>>> >>>>> Please not that function rma is common to Expression, Genome and Exon >>>>> arrays, this I decided to use default settings for Expression arrays, >>>>> since these are still most common. >>>>> >>>>> If you look at the help file for rma you will see the following >>>>> Details: >>>>> Following exonlevel annotations are valid for whole genome arrays: >>>>> core: probesets with category ?unique? and ?mixed?. >>>>> metacore: probesets with category ?unique? only. >>>>> affx: standard AFFX controls. >>>>> all: combination of above. >>>>> >>>>> Thus you need to use e.g. exonlevel="affx+core" >>>>> >>>>> I hope that this information can help you solve your problem. >>>>> >>>>> Best regards >>>>> Christian >>>>> _._._._._._._._._._._._._._._._ >>>>> C.h.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 >>>>> _._._._._._._._._._._._._._._._ >>>>> >>>>> Dick Beyer wrote: >>>>>> Hello help, >>>>>> >>>>>> I'm trying out the xps package and have run into an error I can't >>>>>> seem to workaround for affy Mouse ST MoGene-1_0-st-v1 array data. >>>>>> >>>>>> I've successfully created schemes, plotted raw data and so forth, >>>>>> but rma gives me an error: >>>>>> >>>>>> data.rma <- rma(data.laspada, "laspadaCMRapRMA", tmpdir="", >>>>>> background="pmonly", normalize=TRUE, verbose=TRUE) >>>>>> >>>>>> Error in exonLevel(exonlevel, chiptype) : invalid argument >>>>>> ?exonlevel? >>>>>> >>>>>> Since these are Mouse Gene 1.0 ST Arrays, and the default value for >>>>>> exonlevel="", I'm not sure what I'm doing wrong. >>>>>> >>>>>> Here is the details on my DataTreeSet object, data.laspada: >>>>>> >>>>>> str(data.laspada) >>>>>> Formal class 'DataTreeSet' [package "xps"] with 12 slots >>>>>> ..@ bgtreenames: list() >>>>>> ..@ bgrd :'data.frame': 0 obs. of 0 variables >>>>>> ..@ projectinfo:Formal class 'ProjectInfo' [package "xps"] with 15 >>>>>> slots >>>>>> .. .. ..@ submitter : chr "" >>>>>> .. .. ..@ laboratory : chr "" >>>>>> .. .. ..@ contact : chr "" >>>>>> .. .. ..@ project : list() >>>>>> .. .. ..@ author : list() >>>>>> .. .. ..@ dataset : list() >>>>>> .. .. ..@ source : list() >>>>>> .. .. ..@ sample : list() >>>>>> .. .. ..@ celline : list() >>>>>> .. .. ..@ primarycell : list() >>>>>> .. .. ..@ tissue : list() >>>>>> .. .. ..@ biopsy : list() >>>>>> .. .. ..@ arraytype : list() >>>>>> .. .. ..@ hybridizations:'data.frame': 0 obs. of 0 >>>>>> variables >>>>>> .. .. ..@ treatments :'data.frame': 0 obs. of 0 >>>>>> variables >>>>>> ..@ scheme :Formal class 'SchemeTreeSet' [package "xps"] with >>>>>> 10 slots >>>>>> .. .. ..@ chipname : chr "MoGene-1_0-st-v1" >>>>>> .. .. ..@ chiptype : chr "GenomeChip" >>>>>> .. .. ..@ probeinfo:List of 8 >>>>>> .. .. .. ..$ nrows : int 1050 >>>>>> .. .. .. ..$ ncols : int 1050 >>>>>> .. .. .. ..$ nprobes : int 906151 >>>>>> .. .. .. ..$ ncontrols : int 6682 >>>>>> .. .. .. ..$ ngenes : int 28815 >>>>>> .. .. .. ..$ nunits : int 35557 >>>>>> .. .. .. ..$ nprobesets: int 35557 >>>>>> .. .. .. ..$ naffx : int 22 >>>>>> .. .. ..@ mask :'data.frame': 906151 obs. of 4 variables: >>>>>> .. .. .. ..$ UNIT_ID: int [1:906151] -6682 -6682 -6682 -6682 -6682 >>>>>> -6682 -6682 -6682 -6682 -6682 ... >>>>>> .. .. .. ..$ X : int [1:906151] 673 756 107 466 874 909 137 >>>>>> 868 454 454 ... >>>>>> .. .. .. ..$ Y : int [1:906151] 836 752 279 79 601 446 362 24 >>>>>> 454 288 ... >>>>>> .. .. .. ..$ Mask : int [1:906151] -16 -16 -16 -16 -16 -16 -16 >>>>>> -16 -16 -16 ... >>>>>> .. .. ..@ setname : chr "MoGene-1_0-st-v1" >>>>>> .. .. ..@ settype : chr "scheme" >>>>>> .. .. ..@ rootfile : chr "C:/Program >>>>>> Files/Affymetrix/Library/Scheme_MoGene10stv1r3_na25.root" >>>>>> .. .. ..@ filedir : chr "C:/Program Files/Affymetrix/Library" >>>>>> .. .. ..@ numtrees : int 5 >>>>>> .. .. ..@ treenames:List of 5 >>>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.cxy" >>>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.ann" >>>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.scm" >>>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.idx" >>>>>> .. .. .. ..$ : chr "MoGene-1_0-st-v1.prb" >>>>>> ..@ data :'data.frame': 1102500 obs. of 8 variables: >>>>>> .. ..$ X : int [1:1102500] 0 1 2 >>>>>> 3 4 5 6 7 8 9 ... >>>>>> .. ..$ Y : int [1:1102500] 0 0 0 >>>>>> 0 0 0 0 0 0 0 ... >>>>>> .. ..$ Albert.LaSpada.CM3.07May08.cel_MEAN : int [1:1102500] 4657 >>>>>> 69 4873 104 35 87 5308 83 4819 60 ... >>>>>> .. ..$ Albert.LaSpada.CM4.07May08.cel_MEAN : int [1:1102500] 2986 >>>>>> 49 3194 47 35 37 3339 50 3300 71 ... >>>>>> .. ..$ Albert.LaSpada.CM5.07May08.cel_MEAN : int [1:1102500] 4393 >>>>>> 66 4482 49 41 60 5037 60 5038 51 ... >>>>>> .. ..$ Albert.LaSpada.Rap1.07May08.cel_MEAN: int [1:1102500] 2966 >>>>>> 50 3298 42 33 69 3610 51 3972 83 ... >>>>>> .. ..$ Albert.LaSpada.Rap2.07May08.cel_MEAN: int [1:1102500] 4872 >>>>>> 74 5054 66 41 50 5679 72 5810 65 ... >>>>>> .. ..$ Albert.LaSpada.Rap5.07May08.cel_MEAN: int [1:1102500] 4278 >>>>>> 62 4131 50 28 49 4824 80 4647 57 ... >>>>>> ..@ params : list() >>>>>> ..@ setname : chr "DataSet" >>>>>> ..@ settype : chr "rawdata" >>>>>> ..@ rootfile : chr "E:/home/dbeyer/Microarray/affy bioc >>>>>> xps/laspadaCMRap_cel.root" >>>>>> ..@ filedir : chr "E:/home/dbeyer/Microarray/affy bioc xps" >>>>>> ..@ numtrees : num 6 >>>>>> ..@ treenames :List of 6 >>>>>> .. ..$ : chr "Albert LaSpada CM3 07May08.cel" >>>>>> .. ..$ : chr "Albert LaSpada CM4 07May08.cel" >>>>>> .. ..$ : chr "Albert LaSpada CM5 07May08.cel" >>>>>> .. ..$ : chr "Albert LaSpada Rap1 07May08.cel" >>>>>> .. ..$ : chr "Albert LaSpada Rap2 07May08.cel" >>>>>> .. ..$ : chr "Albert LaSpada Rap5 07May08.cel" >>>>>> >>>>>> And my sessionInfo is: >>>>>> sessionInfo() >>>>>> R version 2.7.0 (2008-04-22) i386-pc-mingw32 >>>>>> >>>>>> locale: >>>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>>>> States.1252;LC_MONETARY=English_United >>>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] xps_1.0.0 >>>>>> >>>>>> I also am using ROOT from root_v5.18.00.win32.tar.gz. >>>>>> >>>>>> Any help or suggestions would be greatly appreciated. >>>>>> >>>>>> Thanks, >>>>>> Dick >>>>>> *************************************************************** **************** >>>>>> Richard P. Beyer, Ph.D. University of Washington >>>>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>>>> Seattle, WA 98105-6099 >>>>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>>>> http://staff.washington.edu/~dbeyer >>>>>> *************************************************************** **************** >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> >> >> > >
ADD REPLYlink written 11.6 years ago by Dick Beyer1.4k
Dear Dick When you look at the Affymetrix libraryfile "MoGene-1_0-st-v1.r3.mps" used for ExpressionConsole you will see that it contains 35557 entries, while the Affymetrix annotation file "MoGene-1_0-st-v1.na25.mm9.transcript.csv" contains 35567 entries. The annotation file contains in column "category" following categories: main, control->affx, control->bgp->antigenomic, normgene->exon, normgene->intron Since "control->bgp->antigenomic, normgene->exon, normgene->intron" have no annotation, I do not use these probesets, which explains the difference to ExpressionConsole. Even if I would use exactly the same probesets as the ExpressionConsole, the results would be different, since ExpressionConsole uses only "Sketch-Quantile" normalization to avoid memory problems, and not the usual quantile normalization. If you want to test if my implementation of the RMA algorithm is correct, please use e.g. HG-U133_Plus_2 data. You will see that you will get the same results as the "affy" package. Best regards Christian Dick Beyer wrote: > Hi Christian, > > Is there a choice of values to the agruments for rma that gets the > same results as Affy Expression Console? I notice that from Affy > Expression Console I get an output with 35557 rows, but with either of > these choices: > > data.rma7 <- rma(data.laspada, > "laspadaCMRapRMA7",tmpdir="",background="antigenomic",normalize=TRUE, > verbose=TRUE,exonlevel="affx+core") > data.rma8 <- rma(data.laspada, > "laspadaCMRapRMA8",tmpdir="",background="antigenomic",normalize=TRUE, > verbose=TRUE,exonlevel="all") > > then validData(data.rma7) or validData(data.rma8) gives me a matrix > with just 28837 rows. > > Thanks very much, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > On Fri, 9 May 2008, cstrato wrote: > >> Dear Dick >> >> I am glad to hear that you could now run rma. >> >> Please feel free to inform me about any potential problems, omissions >> in the help file, or potential improvements. >> >> Best regards >> Christian >> >> >> Dick Beyer wrote: >>> Hi Christian, >>> >>> Thanks for your good help. I'm a repeat offender when it comes to >>> not reading all the way through examples. Thanks for your patience. >>> >>> Using background="antigenomic" made my rma call work just fine. >>> >>> Cheers, >>> Dick >>> ****************************************************************** ************* >>> Richard P. Beyer, Ph.D. University of Washington >>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>> Seattle, WA 98105-6099 >>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>> http://staff.washington.edu/~dbeyer >>> ****************************************************************** ************* >>> On Fri, 9 May 2008, cstrato wrote: >>> >>>> Dear Dick >>>> >>>> Thank you for your tests, which make it clear to me that I need to >>>> improve the help files. >>>> >>>> Since MoGene arrays as well as exon arrays have no MM, you need to >>>> set: background="antigenomic" >>>> >>>> Please have a look at directory "xps/examples" which contains files >>>> "script4xps.R" and "script4exon.R": >>>> In these scripts I give numerous examples which you can copy/paste >>>> and adapt to your needs, especially I describe how to use the >>>> Affymetrix human tissue dataset with arrays HG-U133_Plus_2, >>>> HuGene-1_0-st-v1.r3 and HuEx-1_0-st-v2.r2. >>>> >>>> For HuGene the rma example is as follows: >>>> data.rma <- >>>> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", >>>> >>>> background="antigenomic",normalize=T,exonlevel="metacore+affx") >>>> >>>> Please let me know if these informations could help you solve your >>>> problem. >>>> >>>> Best regards >>>> Christian >>>> >>>> >>>> Dick Beyer wrote: >>>>> Hi Christian, >>>>> >>>>> Thanks for pointing this out. I tried several of the combinations >>>>> listed in the documentation for rma. However, I now get a >>>>> different error message: >>>>> >>>>>> data.rma1 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA1",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="core") >>>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>>> data.rma2 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA2",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="metacore") >>>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>>> data.rma3 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA3",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="affx") >>>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>>> data.rma4 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA4",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="affx+core") >>>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>>> data.rma5 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA5",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="all") >>>>> Error in .local(object, ...) : error in function ?PreprocessRMA? >>>>>> data.rma6 <- >>>>>> rma(data.laspada,"laspadaCMRapRMA6",tmpdir="",background="pmonl y",normalize=TRUE, >>>>>> verbose=TRUE,exonlevel="") >>>>> Error in exonLevel(exonlevel, chiptype) : invalid argument >>>>> ?exonlevel? >>>>> >>>>> Would you please suggest what I could do next? >>>>> Thanks very much, >>>>> Dick >>>>> **************************************************************** *************** >>>>> Richard P. Beyer, Ph.D. University of Washington >>>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>>> Seattle, WA 98105-6099 >>>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>>> http://staff.washington.edu/~dbeyer >>>>> **************************************************************** *************** >>>>> On Fri, 9 May 2008, cstrato wrote:
ADD REPLYlink written 11.6 years ago by cstrato3.9k
Dear Dick After checking my old records I realized that I did indeed compare the output of my package with the output from ExpressionConsole. Here is what I did: Since Affymetrix supplies a user-modifyable meta-probest file *.mps for ExpressionConsole, which in your case will be "MoGene- 1_0-st-v1.r3.mps", I simply replaced the probeset_id and transcript_cluster_id columns with the probest IDs I get from validData(). Running ExpressionConsole with this modified meta-probeset file will show you that the results are almost identical, with the difference due to ExpressionConsole using Sketch-Quantile normalization. I hope this late reply is helpful for you. Best regards Christian Dick Beyer wrote: > Hi Christian, > > Is there a choice of values to the agruments for rma that gets the > same results as Affy Expression Console? I notice that from Affy > Expression Console I get an output with 35557 rows, but with either of > these choices: > > data.rma7 <- rma(data.laspada, > "laspadaCMRapRMA7",tmpdir="",background="antigenomic",normalize=TRUE, > verbose=TRUE,exonlevel="affx+core") > data.rma8 <- rma(data.laspada, > "laspadaCMRapRMA8",tmpdir="",background="antigenomic",normalize=TRUE, > verbose=TRUE,exonlevel="all") > > then validData(data.rma7) or validData(data.rma8) gives me a matrix > with just 28837 rows. > > Thanks very much, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > On Fri, 9 May 2008, cstrato wrote: > >> Dear Dick >> >> I am glad to hear that you could now run rma. >> >> Please feel free to inform me about any potential problems, omissions >> in the help file, or potential improvements. >> >> Best regards >> Christian >> >> >> Dick Beyer wrote: >>> Hi Christian, >>> >>> Thanks for your good help. I'm a repeat offender when it comes to >>> not reading all the way through examples. Thanks for your patience. >>> >>> Using background="antigenomic" made my rma call work just fine. >>> >>> Cheers, >>> Dick >>> ****************************************************************** ************* >>> Richard P. Beyer, Ph.D. University of Washington >>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>> Seattle, WA 98105-6099 >>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>> http://staff.washington.edu/~dbeyer >>> ****************************************************************** ************* >>> On Fri, 9 May 2008, cstrato wrote: >>> >>>> Dear Dick >>>> >>>> Thank you for your tests, which make it clear to me that I need to >>>> improve the help files. >>>> >>>> Since MoGene arrays as well as exon arrays have no MM, you need to >>>> set: background="antigenomic" >>>> >>>> Please have a look at directory "xps/examples" which contains files >>>> "script4xps.R" and "script4exon.R": >>>> In these scripts I give numerous examples which you can copy/paste >>>> and adapt to your needs, especially I describe how to use the >>>> Affymetrix human tissue dataset with arrays HG-U133_Plus_2, >>>> HuGene-1_0-st-v1.r3 and HuEx-1_0-st-v2.r2. >>>> >>>> For HuGene the rma example is as follows: >>>> data.rma <- >>>> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", >>>> >>>> background="antigenomic",normalize=T,exonlevel="metacore+affx") >>>> >>>> Please let me know if these informations could help you solve your >>>> problem. >>>> >>>> Best regards >>>> Christian
ADD REPLYlink written 11.6 years ago by cstrato3.9k
Hi Christian, Thanks for the update. I was planning on figuring out what the probset difference was between xps and ExpresionConsole, so thanks for saving me that effort. I appreciate it. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Wed, 14 May 2008, cstrato wrote: > Dear Dick > > After checking my old records I realized that I did indeed compare the output > of my package with the output from ExpressionConsole. Here is what I did: > > Since Affymetrix supplies a user-modifyable meta-probest file *.mps for > ExpressionConsole, which in your case will be "MoGene- 1_0-st-v1.r3.mps", I > simply replaced the probeset_id and transcript_cluster_id columns with the > probest IDs I get from validData(). Running ExpressionConsole with this > modified meta-probeset file will show you that the results are almost > identical, with the difference due to ExpressionConsole using Sketch-Quantile > normalization. > > I hope this late reply is helpful for you. > > Best regards > Christian > > Dick Beyer wrote: >> Hi Christian, >> >> Is there a choice of values to the agruments for rma that gets the same >> results as Affy Expression Console? I notice that from Affy Expression >> Console I get an output with 35557 rows, but with either of these choices: >> >> data.rma7 <- rma(data.laspada, >> "laspadaCMRapRMA7",tmpdir="",background="antigenomic",normalize=TRUE, >> verbose=TRUE,exonlevel="affx+core") >> data.rma8 <- rma(data.laspada, >> "laspadaCMRapRMA8",tmpdir="",background="antigenomic",normalize=TRUE, >> verbose=TRUE,exonlevel="all") >> >> then validData(data.rma7) or validData(data.rma8) gives me a matrix with >> just 28837 rows. >> >> Thanks very much, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ******************************************************************* ************ >> On Fri, 9 May 2008, cstrato wrote: >> >>> Dear Dick >>> >>> I am glad to hear that you could now run rma. >>> >>> Please feel free to inform me about any potential problems, omissions in >>> the help file, or potential improvements. >>> >>> Best regards >>> Christian >>> >>> >>> Dick Beyer wrote: >>>> Hi Christian, >>>> >>>> Thanks for your good help. I'm a repeat offender when it comes to not >>>> reading all the way through examples. Thanks for your patience. >>>> >>>> Using background="antigenomic" made my rma call work just fine. >>>> >>>> Cheers, >>>> Dick >>>> ***************************************************************** ************** >>>> Richard P. Beyer, Ph.D. University of Washington >>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>> Seattle, WA 98105-6099 >>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>> http://staff.washington.edu/~dbeyer >>>> ***************************************************************** ************** >>>> On Fri, 9 May 2008, cstrato wrote: >>>> >>>>> Dear Dick >>>>> >>>>> Thank you for your tests, which make it clear to me that I need to >>>>> improve the help files. >>>>> >>>>> Since MoGene arrays as well as exon arrays have no MM, you need to >>>>> set: background="antigenomic" >>>>> >>>>> Please have a look at directory "xps/examples" which contains files >>>>> "script4xps.R" and "script4exon.R": >>>>> In these scripts I give numerous examples which you can copy/paste and >>>>> adapt to your needs, especially I describe how to use the Affymetrix >>>>> human tissue dataset with arrays HG-U133_Plus_2, HuGene- 1_0-st-v1.r3 >>>>> and HuEx-1_0-st-v2.r2. >>>>> >>>>> For HuGene the rma example is as follows: >>>>> data.rma <- >>>>> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="", >>>>> background="antigenomic",normalize=T,exonlevel="metacore+affx") >>>>> >>>>> Please let me know if these informations could help you solve your >>>>> problem. >>>>> >>>>> Best regards >>>>> Christian > >
ADD REPLYlink written 11.6 years ago by Dick Beyer1.4k
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