[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
Dick Beyer
dbeyer at u.washington.edu
Fri May 9 19:33:58 CEST 2008
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
>> *******************************************************************************
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