[BioC] lumi, lumiHumanV2 and GOstats

[James W. MacDonald]

Hi Al,

Al Ivens wrote:
> 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,
> 
> a
> 
> X---------------------------------------------------------
> Error in do.call(paste(pname, "dbconn", sep = "_"), list()) : 
>   could not find function "lumiHumanV2_dbconn"

This is because there isn't a lumiHumanV2 in BioC 2.2. Not sure how you 
got this installed, as biocLite() shouldn't have done so.

Anyway, I believe you want the lumiHumanAll.db package (and to remove 
the lumiHumanV2 package, as that is from an older BioC release).

Best,

Jim


>>
>> 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", 
>        "hyperGTest")
> 1: hyperGTest(BPparams)
>> sessionInfo()
> R version 2.7.0 (2008-04-22) 
> x86_64-pc-linux-gnu 
> 
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATI
> ON=C
> 
> 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
> 
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623