[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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>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives: 
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> 
>> 
>
>



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