pd.mapping50k.xba240を作る

R SNP

BioCのSNPchip*1を試すのに必要なので作り方を調べた。

library(makePlatformDesign)
makePDpackage("Mapping50K_Xba240.CDF",
"Mapping50K_Xba240_probe_fasta",
"Mapping50K_Xba240.na22.annot.csv",
type="SNP")

必要なファイルは、
http://www.affymetrix.com/support/technical/byproduct.affx?product=100k
から取得できた。
CDF
# Library Files
# Mapping 50K Hind 240 Array (zip, 16 MB)
probe_fasta
# Sequence Files
# Mapping50K_Xba240 Flanking Sequences, Fasta
annot.csv
# ALIGNMENT, ANNOTATION, AND SEQUENCE FILES
# Mapping50K_Xba240 Annotations, CSV format (11 MB, 3/9/07)
makePDpackageめっさ時間かかる。

sudo R CMD INSTALL pdmapping50kxba240 # => まだ試してない

<追記>朝来たら失敗してた‥orz

affymetrix SNP 
The package will be called pd.mapping50k.xba240 
Reading Mapping50K_Xba240.CDF 
Creating environment...........................................................R(5247,0xa000cfc0) malloc: *** vm_allocate(size=20484096) failed (error code=3)
R(5247,0xa000cfc0) malloc: *** error: can't allocate region
R(5247,0xa000cfc0) malloc: *** set a breakpoint in szone_error to debug
Done.
the part of the args list of 'list' being evaluated was:
   (feature_type = list(description = "This column distinguishes PM and MM features.\nAnything else is left as an NA", levels = list(PM = "Perfect Match probe", MM = "Mismatch probe")), allele = list(description = "calls", levels = list(A = "A", T = "T", G = "G", C = "C")), target_strand = list(description = "Target Strandness", levels = list(Sense = "Sense", Antisense = "Antisense")), snp_location = list(description = "location of the SNP"), )
 以下にエラーinitialize(value, ...) :  要素 5 が空です

*1:Affymetrix Mapping arrayのビジュアライズ用パッケージ