[BioC] vennSelect problem with hgu133plus package

[James W. MacDonald]

Hi Maxim,

You want an annotation package, which for a few years now have a .db 
appended to the name. So try

biocLite("hgu133plus2.db")

and then re-run your analysis.

Best,

Jim



Maxim wrote:
> Hi,
> 
> 
> I have a problem to understand what I type of variables I have to feed into
> the function vennSelect. As the vennDiagram is only able to get the overlap
> between multiple contrasts depending on the p.value (btw: can I use the
> decideTests function dependent on the adj.p.value, too?), I took a look at
> the vennSelect function which appears to be made for extactly this case.
> What I did:
> 
> 
> 
> a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose =
> TRUE)
> 
> x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn",
> normalize.param
> 
> = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method =
> 
> "medianpolish")
> 
> 
> design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3)))
> 
> colnames(design) <- c("control", "four", "sixteen")
> 
> fit <- lmFit(x, design)
> 
> 
> contrast.matrix <- makeContrasts(four-control, sixteen-control,
> levels=design)
> 
> 
> fit2 <- contrasts.fit(fit, contrast.matrix)
> 
> fit2 <- eBayes(fit2)
> 
> 
> results <- decideTests(fit2)
> 
> 
> Now I try:
> 
> vennSelect(x,design,results,contrast.matrix,fit2)
> 
> 
> but I get:
> 
> 
> Loading required package: hgu133plus2
> 
> Error in aaf.handler(chip = chip) :
> 
>   Couldn't load data package hgu133plus2
> 
> In addition: Warning message:
> 
> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return
> = TRUE,  :
> 
>   there is no package called 'hgu133plus2'
> 
> 
> unfortunately it seems I cannot install hgu133plus2:
> 
> biocLite("hgu133plus2")
> 
> Running biocinstall version 2.3.14 with R version 2.8.1
> 
> Your version of R requires version 2.3 of Bioconductor.
> 
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
> 
>   argument 'lib' is missing: using '/Users/maxim/Library/R/2.8/library'
> 
> Warning message:
> 
> package ‘hgu133plus2’ is not available
> 
> 
> What is wrong?
> 
> 
> Maxim
> 
> 
> 
> sessionInfo()
> 
> R version 2.8.1 (2008-12-22)
> 
> i386-apple-darwin8.11.1
> 
> 
> locale:
> 
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> 
> attached base packages:
> 
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> methods   base
> 
> 
> other attached packages:
> 
>  [1] affycoretools_1.14.1 annaffy_1.14.0       KEGG.db_2.2.5
> gcrma_2.14.1         matchprobes_1.14.1
> 
>  [6] biomaRt_1.16.0       GOstats_2.8.0        Category_2.8.4
> genefilter_1.22.0    survival_2.34-1
> 
> [11] RBGL_1.18.0          annotate_1.20.1      xtable_1.5-4
> GO.db_2.2.5          graph_1.20.0
> 
> [16] hgu133plus2cdf_2.3.0 hgu133plus2.db_2.2.5 RSQLite_0.7-1
> DBI_0.2-4            AnnotationDbi_1.4.2
> 
> [21] gplots_2.6.0         gdata_2.4.2          gtools_2.5.0-1
> vsn_3.8.0            lattice_0.17-17
> 
> [26] limma_2.16.5         affy_1.20.2          Biobase_2.2.1
> 
> 
> loaded via a namespace (and not attached):
> 
> [1] GSEABase_1.4.0       RCurl_0.94-1         XML_2.3-0
> affyio_1.10.1        cluster_1.11.11
> 
> [6] grid_2.8.1           preprocessCore_1.4.0
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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