[BioC] Question on copy number estimation for Affymetrix SNP array 100k and 500k

[Henrik Bengtsson]

Hi,

regarding your question on aroma.affymetrix;  The aroma.* framework
use a well-defined an strict directory and filename convention for
locating data file sets and annotation data files.  It seems to me
that you haven't placed the CDF for your chip type in the correct
directory.  This is all explained at

   http://www.aroma-project.org/

under the 'Get started' section (and subsection 'Setup').

For future questions related to aroma.affymetrix, please use its
dedicated mailing list/forum;

  http://www.aroma-project.org/forum/

Hope this helps

/Henrik

On Mon, Sep 20, 2010 at 3:27 PM, Zhu, Julie <Julie.Zhu at umassmed.edu> wrote:
> Hi,
>
> The crlmm package implements copy number estimation for Affymetrix SNP 6.0
> platform. The genoCN package has functions for identification of copy number
> states for Illumina SNP array.
>
> I am wondering how I could adopt crlmm package or geneoCN package to
> estimate copy number for the old Affymetrix SNP platforms (100k and 500k)
> using CEL files as input.
>
> I also tried aroma.Affymetrix and aroma.cn but encountered the following
> error even though the directory Nsp_CEL_CML does contain the CEL files with
> chip type of Mapping250K_Nsp.
>
> Thank you very much for your help!
>
> Best regards,
>
> Julie
>
> library(aroma.affymetrix)
> library(aroma.cn)
> cs <- AffymetrixCelSet$byName("Nsp_CEL_CML", chipType="Mapping250K_Nsp")
> Error in list(`AffymetrixCelSet$byName("Nsp_CEL_CML", chipType =
> "Mapping250K_Nsp")` = <environment>,  :
>
> [2010-09-20 17:21:12] Exception: Could not locate a file for this chip type:
> Mapping250K_Nsp
>  at throw(Exception(...))
>  at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipType, tags),
>  at throw("Could not locate a file for this chip type: ", paste(c(chipType,
> tags), collaps
>  at method(static, ...)
>  at AffymetrixCdfFile$byChipType(chipType)
>  at method(static, ...)
>  at AffymetrixCelSet$byName("Nsp_CEL_CML", chipType = "Mapping250K_Nsp")
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] geneplotter_1.26.0       lattice_0.18-8           annotate_1.26.1
>  [4] AnnotationDbi_1.10.2     pd.mapping250k.nsp_1.0.0 RSQLite_0.9-2
>  [7] DBI_0.2-5                aroma.cn_0.5.0
> aroma.affymetrix_1.7.0
> [10] aroma.apd_0.1.7          affxparser_1.20.0        R.huge_0.2.0
> [13] aroma.core_1.7.0         aroma.light_1.16.1       matrixStats_0.2.1
> [16] R.rsp_0.4.0              R.cache_0.3.0            R.filesets_0.9.0
> [19] digest_0.4.2             R.utils_1.5.2            R.oo_1.7.3
> [22] oligo_1.12.2             R.methodsS3_1.2.0        VanillaICE_1.10.0
> [25] IRanges_1.6.11           crlmm_1.6.5              oligoClasses_1.10.0
> [28] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.16.0         Biostrings_2.16.9     bit_1.1-4
>  [4] ellipse_0.3-5         ff_2.1-2              genefilter_1.30.0
>  [7] grid_2.11.1           KernSmooth_2.23-3     mvtnorm_0.9-92
> [10] preprocessCore_1.10.0 RColorBrewer_1.0-2    splines_2.11.1
> [13] survival_2.35-8       tools_2.11.1          xtable_1.5-6
>
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