[BioC] Category package problems with Vignette documentation

Neefs, Jean-Marc [PRDBE] JNEEF1 at PRDBE.jnj.com
Tue Jun 7 13:56:07 CEST 2005

Dear Bioconductor,

I have installed the Category package 1.0.1 on my Windows 2000 computer,
after installation of R 2.1.0 and other packages required by Category
(Biobase 1.5.12; tools -- not listed in R package list; genefilter 1.6.2
actually loads 1.6.1; KEGG 1.8.1; hgu95av2 1.8.4; ALL 1.0.2; survival 2.17;
splines -- no longer listed in Bioconductor package list)

I would like to use the Category package for microarray data analysis. I am
not an experienced R user, so I get easily confused.

The Category vignette code works well until line:
> Amat = t(PWAmat("hgu95av2"))
where PWAmat is a function from the 'annotate' package -- not uploaded by
Category and no error reported when loading the Category package.
I could find a fix by loading and installing 'annotate' from local zip file.

Could you make 'Category' report an error when 'annotate' is not loaded?

Also could you point me to the latest 'splines' package or any other that
replaces it? -- I found 'splines' yesterday morning but no longer yesterday

Then the code breaks again at line:
> tA = AmER2 %*% tobs$statistic
generates Error: Object "tobs" not found

I suppose 'tobs' is a matrix calculated from 'ttests' described higher in
the vignette, because of the matrix multiplication operator. I tried:
> tA = AmER2 %*% ttests$statistic
which is probably silly because it generates: Error in AmER2 %*%
ttests$statistic : non-conformable arguments

Could you include in the vignette the code to obtain 'tobs' and send me a

Thank you very much in advance for your kind help,


Jean-Marc Neefs, PhD
Senior Bioinformatics Specialist
Johnson&Johnson PRD, Janssen Pharmaceutica
30 Turnhoutseweg,
B-2340 Beerse

tel +32 14 60 6084
fax +32 14 60 3226
eml jneef1 at prdbe.jnj.com

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