[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
Dick Beyer
dbeyer at u.washington.edu
Fri May 9 20:59:20 CEST 2008
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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