[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
cstrato
cstrato at aon.at
Fri May 9 21:12:58 CEST 2008
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
>>>>> *******************************************************************************
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
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