[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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