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

I have seen this issue when the installation of the annotation package was not 100% fine. Can you please try reinstalling it? (make sure you've got enough free space on disk) source("http://www.bioconductor.org/biocLite.R") biocLite("pd.huex.1.0.st.v2") The one other time I saw this happening was when the packages were being installed a a remote disk (like NFS mounts) with low performance. benilton 2014-05-18 17:52 GMT-03:00 Aaerp <al3n70rn@gmail.com>: > 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 > -- [image: Benilton Carvalho on about.me] Benilton Carvalho about.me/benilton <http: about.me="" benilton=""> [[alternative HTML version deleted]]