[BioC] Error when trying to normalize human Exon arrays (pd.huex.1.0.st.v2)

Aaerp al3n70rn at gmail.com
Sun May 18 22:52:01 CEST 2014


Hi,

I am having this error when I try to perform rma normalization in human 
exon affymetrix arrays.

Here is my code:

  library('oligo')
  library('pd.huex.1.0.st.v2')

  celFiles = list.celfiles("~/43107_status",full.name=T)

  raw = read.celfiles (celFiles, pkgname = 'pd.huex.1.0.st.v2')

  eset_core = rma(raw, target = "core")

Error in sqliteFetch(rs, n = -1, ...) :
   RSQLite driver: (RS_SQLite_fetch: failed first step: database disk 
image is malformed)

  sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
  [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4 DBI_0.2-7               
oligo_1.28.1 Biostrings_2.32.0
  [6] XVector_0.4.0           IRanges_1.22.6 Biobase_2.24.0          
oligoClasses_1.26.0 BiocGenerics_0.10.0

loaded via a namespace (and not attached):
  [1] affxparser_1.36.0     affyio_1.32.0 BiocInstaller_1.14.2  
bit_1.1-12            codetools_0.2-8 ff_2.2-13
  [7] foreach_1.4.2         GenomeInfoDb_1.0.2 GenomicRanges_1.16.3  
iterators_1.0.7       preprocessCore_1.26.1 splines_3.1.0
[13] stats4_3.1.0          tools_3.1.0           zlibbioc_1.10.0

Any clues to what is wrong?

Agusti



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