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

[Zhu, Julie]

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