[BioC] Problems with oligo and pd.genomewidesnp.6

[Vincent Carey 525-2265]

i am able to reproduce this error in the devel line.  very surprising
because we have some unit tests for the pd.genomewide* but
apparently they have not been run.  i will try to get to the bottom
of this.  if the pd.genomewide* have to be rebuilt it may take a
couple of days to push out a revision.

1: justSNPRMA(list.celfiles())
2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package =
3: readChar(con, 5, useBytes = TRUE)

Selection: 0
> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-05-18 r45723)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
 [1] pd.genomewidesnp.6_0.4.1 oligo_1.5.2              oligoClasses_1.3.3
 [4] affxparser_1.13.3        AnnotationDbi_1.1.35     preprocessCore_1.3.0
 [7] RSQLite_0.6-8            DBI_0.2-4                Biobase_2.1.3
[10] weaver_1.5.0             codetools_0.1-3          digest_0.3.1


---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Fri, 23 May 2008, Jeremy Silver wrote:

> Hello,
>
> I'm trying to call genotypes from Affymetrix SNP 6.0 chips using the
> oligo package. I've run into a small problem, that I think may be due to
> the differences between the bioconductor package pd.genomewidesnp.6 and
> the other pd.*.* annotation packages. Details are below. Any ideas?
>
> Thanks,
>
> Jeremy
>
> ###############################################
>
> # here are the names of the .CEL files
>
>  > fullFilenamesOrigCelFiles[1:5]
> [1] "rawData/tds2008/GenomeWideSNP_6/SNP001_01_M001A.CEL"
> [2] "rawData/tds2008/GenomeWideSNP_6/SNP001_02_M003A.CEL"
> [3] "rawData/tds2008/GenomeWideSNP_6/SNP001_03_M007A.CEL"
> [4] "rawData/tds2008/GenomeWideSNP_6/SNP001_04_M015A.CEL"
> [5] "rawData/tds2008/GenomeWideSNP_6/SNP001_06_M026A.CEL"
>
> # call justSNPRMA
>
>  > snpRmaResults <- justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5],
> +                             verbose = TRUE,
> +                             phenoData = NULL,
> +                             normalizeToHapmap = TRUE)
> Reading CEL files.
> Normalizing to Hapmap.
> Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
> In addition: Warning message:
> In readChar(con, 5L, useBytes = TRUE) :
>   cannot open compressed file '', probable reason 'No such file or
> directory'
>  > traceback()
> 3: readChar(con, 5L, useBytes = TRUE)
> 2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""),
>        package = pkgname))
> 1: justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], verbose = TRUE,
>        phenoData = NULL, normalizeToHapmap = TRUE)
>  > sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] pd.genomewidesnp.6_0.4.1 aroma.affymetrix_0.9.1
> aroma.apd_0.1.3
>  [4] R.huge_0.1.5             digest_0.3.1
> aroma.light_1.7.2
>  [7] R.rsp_0.3.4              R.cache_0.1.7
> R.utils_1.0.2
> [10] R.oo_1.4.3               R.methodsS3_1.0.1
> oligo_1.4.0
> [13] oligoClasses_1.2.0       affxparser_1.11.14
> AnnotationDbi_1.2.1
> [16] preprocessCore_1.1.9     RSQLite_0.6-8
> DBI_0.2-4
> [19] Biobase_1.99.10
>
> # See if we can find the problem - the following three lines come from
> justSNPRMA
>
>  > filenames <- fullFilenamesOrigCelFiles[1:5]
>  >     headdetails <- readCelHeader(filenames[1])
>  >    pkgname <- cleanPlatformName(headdetails[["chiptype"]])
>
> # The problematic line asks to load the following file....
>
>  > system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package =
> pkgname)
> [1] ""
>
> # ... which doesn't seem to exist. Here's the folder we're looking at
>
>  > system.file("extdata", package = pkgname)
> [1] "$HOME/R/i686-pc-linux-gnu-library/2.7/pd.genomewidesnp.6/extdata"
>
> # ... and here are the files it contains
>
>  > list.files(system.file("extdata", package = pkgname))
> [1] "pd.genomewidesnp.6.sqlite" "seqMat.rda"
>
> Looks like we were trying to load a file called
> "pd.genomewidesnp.6Ref.rda" from this folder.
>
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