[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’

cstrato cstrato at aon.at
Fri May 9 13:35:11 CEST 2008


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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