[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’
Dick Beyer
dbeyer at u.washington.edu
Sat May 10 00:42:47 CEST 2008
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
>>>>>> *******************************************************************************
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>
>>>>
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>>>>
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>>>
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