[BioC] lumi, lumiHumanV2 and GOstats

[Al Ivens]

Hi Jim,

Ah.  That explains it, many thanks.  And no, biocLite wasnt guilty!

Cheers,

a

> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 29 May 2008 14:44
> To: Al Ivens
> Cc: 'bioc'
> Subject: Re: [BioC] lumi, lumiHumanV2 and GOstats
> 
> 
> 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_ID
> ENTIFICATI
> > 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
> 




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