[BioC] lumi, lumiHumanV2 and GOstats

Al Ivens alicat at sanger.ac.uk
Thu May 29 15:34:02 CEST 2008

Hi all,

I have been trying out the GOstats section of the lumi vignette, using
data obtained from Illumina WG6 chips.  I use the lumiHumanV2 package.

I have two installations of R and Bioconductor:

1. On my Windoze laptop, I have R 2.6.2 and as far as I am aware, up to
date versions of the relevant Bioconductor packages for 2.6.2.  Doing
the GOstats works just fine.
2. On my Unix server, I have R 2.7.0, and as far as I am aware, the most
up to date Bioc packages.  Doing the GOstats on this platform, using the
same GOstats script etc, doesn't work.

Below is the error, traceback and sessionInfo.  At a bit of loss as to
why the difference!

Cheers and thanks in advance for any assistance,


Error in do.call(paste(pname, "dbconn", sep = "_"), list()) : 
  could not find function "lumiHumanV2_dbconn"
> traceback()
8: do.call(paste(pname, "dbconn", sep = "_"), list())
7: getGoToEntrezMap_db(p)
6: categoryToEntrezBuilder(p)
5: categoryToEntrezBuilder(p)
4: is(object, Cl)
3: is(object, Cl)
2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", 
1: hyperGTest(BPparams)
> sessionInfo()
R version 2.7.0 (2008-04-22) 


attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils

 [8] datasets  methods   base     

other attached packages:
 [1] arrayQualityMetrics_1.6.0 beadarray_1.8.0          
 [3] latticeExtra_0.3-1        simpleaffy_2.16.0        
 [5] affyPLM_1.16.0            gcrma_2.12.0             
 [7] matchprobes_1.12.0        RColorBrewer_1.0-2       
 [9] vsn_3.6.0                 geneplotter_1.18.0       
[11] lattice_0.17-2            gplots_2.6.0             
[13] gdata_2.4.1               gtools_2.4.0             
[15] limma_2.14.1              GOstats_2.6.0            
[17] Category_2.6.0            genefilter_1.20.0        
[19] survival_2.34             RBGL_1.16.0              
[21] annotate_1.18.0           xtable_1.5-2             
[23] GO.db_2.2.0               AnnotationDbi_1.2.1      
[25] RSQLite_0.6-8             DBI_0.2-4                
[27] graph_1.18.1              lumiHumanV2_1.3.1        
[29] lumi_1.6.0                mgcv_1.3-31              
[31] affy_1.18.0               preprocessCore_1.2.0     
[33] affyio_1.8.0              Biobase_2.0.1            

loaded via a namespace (and not attached):
[1] cluster_1.11.9     KernSmooth_2.22-21

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