[BioC] Problem creating expression set.

[James W. MacDonald]

You need to have consistent ordering between your phenoData and 
expression matrix.

Best,

Jim



On 5/1/2012 1:18 PM, dha 2001 wrote:
> Hi,
>
> I'm trying to create a small expression set from the following pieces of
> data:
>
>
>> is.matrix(sdr)
> [1] TRUE
>
>
>> sdr
>                   PR8.16      PR8.12    X31.12    PR8.24     VN.24     VN.12
> 1600014C10Rik 0.1398317 -0.07606908 0.1183433 0.8794916 0.5701783 0.2045793
> 1700123I01Rik 0.2797059  0.17511382 0.2417623 0.9663656 0.7656528 0.3691544
> 2010005H15Rik 0.5722452  0.22999830 0.5018363 1.0000000 0.7351083 0.5912760
>                   X31.16     VN.16    X31.24 M.12       M.24        M.16
> 1600014C10Rik 0.3294323 0.1177338 1.0000000    0 -0.1618993 -0.07646396
> 1700123I01Rik 0.4761550 0.4523119 1.0000000    0  0.3090218  0.16773738
> 2010005H15Rik 0.8050344 0.5789556 0.8703344    0  0.1371578  0.06224045
>
>
> And
>
>
>> repPhenoData
> An object of class "AnnotatedDataFrame"
>    rowNames: X31.12 PR8.24 ... VN.24 (12 total)
>    varLabels: strain time
>    varMetadata: labelDescription
>> pData(repPhenoData)
>         strain time
> X31.12    X31   12
> PR8.24    PR8   24
> PR8.12    PR8   12
> PR8.16    PR8   16
> VN.16      VN   16
> M.12        M   12
> M.24        M   24
> X31.24    X31   24
> VN.12      VN   12
> M.16        M   16
> X31.16    X31   16
> VN.24      VN   24
>
> As far as I can tell, the names match up:
>
>> sort(sampleNames(repPhenoData))
>   [1] "M.12"   "M.16"   "M.24"   "PR8.12" "PR8.16" "PR8.24" "VN.12"  "VN.16"
>   [9] "VN.24"  "X31.12" "X31.16" "X31.24
>
>> sort(colnames(sdr))
>   [1] "M.12"   "M.16"   "M.24"   "PR8.12" "PR8.16" "PR8.24" "VN.12"  "VN.16"
>   [9] "VN.24"  "X31.12" "X31.16" "X31.24"
>
> The objects appear to be valid:
>
>> validObject(sdr)
> [1] TRUE
>> validObject(repPhenoData)
> [1] TRUE
>
> However, when I try to create the expression set, I get:
>
>> eSDR<- new("ExpressionSet", exprs=sdr, phenoData=repPhenoData)
> Error in validObject(.Object) :
>    invalid class "ExpressionSet" object: sampleNames differ between
> assayData and phenoData
>
>
> Any clues?
>
> Thanks!
>
> -DHA
>
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ggplot2_0.9.0  Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>   [1] MASS_7.3-17        RColorBrewer_1.0-5 colorspace_1.1-1
> dichromat_1.2-4
>   [5] digest_0.5.2       grid_2.14.2        memoise_0.1        munsell_0.3
>
>   [9] plyr_1.7.1         proto_0.3-9.2      reshape2_1.2.1     scales_0.2.0
>
> [13] stringr_0.6        tools_2.14.2
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099