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 >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> >> >> > >