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

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