[BioC] oligo package: extracting position, sequence, and intensity from Affymetrix tiling array

[Cindy [guest]]

Dear Bioconductor team, 
 
I am currently using the oligo package for analyzing tiling array data (Affymetrix GeneChip Human Tiling 2.0R Array). I made a PlatformDesign package (pd.hs35b.p02r.v01_0.0.1) using the makePdInfoPackage function from pdInfoBuilder package. The .bpmap file used to make this package was downloaded from the Affymetrix website at http://www.affymetrix.com/analysis/downloads/lf/tiling/Hs35b_PR_v01-3_NCBIv36.bpmap.zip

seed <- new(
    "AffyTilingPDInfoPkgSeed",
    bpmapFile = bpmap,
    celFile = celfile,
    author = "Cindy Yao",
    biocViews = "AnnotationData",
    genomebuild = "NCBI Build 36",
    organism = "Human",
    species = "Homo Sapiens"
    );
    
# create package
makePdInfoPackage(seed, destDir = cfg$platform.design.directory);

I was able to read in the cel files using the read.celfiles; however, I came across a problem when I try to extract information about the probe position, sequence and which chromosome it belongs to. It appears that the length of the chromosome vector doesn't equal to the length of the position vector and the number of rows from the intensity data. The code that I used is displayed below as well as the respective structures of each object:

data <- read.celfiles(ArrayFiles);
 
pm.data     <- pm(data); 
pm.chr      <- pmChr(data); 
pm.position <- pmPosition(data); 
 
str(pm.data) 
 num [1:6003165, 1:10] 56 73 155 98 60 103 91 184 176 110 ... 
 - attr(*, "dimnames")=List of 2 
  ..$ : chr [1:6003165] "2566" "2567" "2568" "2569" ... 
  ..$ : chr [1:10] "1_10_(Hs35b_P02R_v01).CEL" "1_11_(Hs35b_P02R_v01).CEL" "1_12_(Hs35b_P02R_v01).CEL" "1_13_(Hs35b_P02R_v01).CEL" ... 
 
str(pm.chr) 
 chr [1:6002540] "chr2" "chr9" "chr2" "chr2" "chr9" "chr9" ... 
 
str(pm.position) 
 int [1:6003165] 80928567 125675126 6587123 22535130 20912500 118746438 138140160 130174378 202638022 133066609 ... 

I am not sure where the problem is. Could someone help me out? Thank you very much for your time!

Best,
Cindy

 -- output of sessionInfo(): 

R version 2.14.2 (2012-02-29)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  methods   utils     base     

other attached packages:
[1] pd.hs35b.p02r.v01_0.0.1 RSQLite_0.11.1          DBI_0.2-5              
[4] affxparser_1.26.4       oligo_1.18.1            oligoClasses_1.16.0    
[7] Biobase_2.14.0         

loaded via a namespace (and not attached):
[1] Biostrings_2.22.0     IRanges_1.12.6        affyio_1.22.0        
[4] bit_1.1-8             ff_2.2-5              preprocessCore_1.16.0
[7] splines_2.14.2        tools_2.14.2          zlibbioc_1.0.1

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