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

[Dick Beyer]

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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