[BioC] error preProcessGeneST ArrayTools (R 2.15.2, BioC 2.11)
José LÓPEZ
jose.lopez at umh.es
Thu Dec 20 18:20:42 CET 2012
Dear all,
I was trying to use preProcessGeneST ArrayTools to get rid of control probes in Mouse Gene 1.0ST arrays, but it dosent work in last R/BioC version.
It was working perfectly in previous R/BioC version. Do I downgrade to previous version to continue to use the ArrayTools package?
It is possible that the error has a different cause?
Thank you for your kind help,
> eset_process = preProcessGeneST(eset_norm, output = TRUE)
Warning message:
In chkPkgs(chip) :
The mogene10sttranscriptcluster.db package does not appear to contain annotation data.
Error in function (x, envir, mode = "any", ifnotfound = list(function(x) stop(paste0("value for '", :
error in evaluating the argument 'envir' in selecting a method for function 'mget': Error: object 'mogene10sttranscriptclusterMAP' not found
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] mogene10stv1cdf_2.11.0 annaffy_1.30.0 KEGG.db_2.8.0
[4] GO.db_2.8.0 arrayQualityMetrics_3.14.0 ArrayTools_1.18.0
[7] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.8.0 RSQLite_0.11.2
[10] DBI_0.2-5 affy_1.36.0 annotate_1.36.0
[13] AnnotationDbi_1.20.3 vsn_3.26.0 Biobase_2.18.0
[16] BiocGenerics_0.4.0 limma_3.14.3
loaded via a namespace (and not attached):
[1] affyio_1.26.0 affyPLM_1.34.0 beadarray_2.8.1 BeadDataPackR_1.10.0 BiocInstaller_1.8.3
[6] Biostrings_2.26.2 Cairo_1.5-2 cluster_1.14.3 colorspace_1.2-0 gcrma_2.30.0
[11] genefilter_1.40.0 grid_2.15.2 Hmisc_3.10-1 hwriter_1.3 IRanges_1.16.4
[16] lattice_0.20-10 latticeExtra_0.6-24 parallel_2.15.2 plyr_1.8 preprocessCore_1.20.0
[21] RColorBrewer_1.0-5 reshape2_1.2.2 setRNG_2011.11-2 splines_2.15.2 stats4_2.15.2
[26] stringr_0.6.2 survival_2.37-2 SVGAnnotation_0.93-1 tools_2.15.2 XML_3.95-0.1
[31] xtable_1.7-0 zlibbioc_1.4.0
> class(H2Bgfp_norm)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
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