[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
cstrato
cstrato at aon.at
Fri May 9 20:13:43 CEST 2008
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
>>> *******************************************************************************
>>> _______________________________________________
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>>>
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