[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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