Thank you very much for the report.

Issue fixed on oligo 1.18.2... which may become available in 1 or 2 days...
Note that a new BioC (v 2.10) will be released very very soon and this
issue is already addressed for the new release as well.

Thanks, benilton

On 30 March 2012 04:02, Cindy [guest] <guest@bioconductor.org> wrote:

>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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