[BioC] Annotation packages

[Sim, Fraser]

Thanks. I tried to repeat ommiting the "-" but got the same error
message.

-----Original Message-----
From: laurent [mailto:lgautier at gmail.com] 
Sent: Thursday, October 30, 2008 5:21 PM
To: Sim, Fraser
Cc: Sean Davis; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Annotation packages

"-" might not be a valid character for package names
(or I'd remember it did not use to be)


L.


On Thu, 2008-10-30 at 17:12 -0400, Sim, Fraser wrote:
> I tried to follow the instructions. I thought it had successfully made
an annotation package but I can't load it. See code and results below.
The error says it is not a valid package. Any ideas?
> 
> > makeHUMANCHIP_DB(affy = FALSE, 
> +  prefix = "hgu95a-e2",
> +  fileName = "extdata.txt",
> +  baseMapType = "eg",
> +  version = "1.0.0",
> +  manufacturer = "Affymetrix",
> +  chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e",
> +  manufacturerUrl = "http://www.affymetrix.com")
> baseMapType is eg
> Prepending Metadata
> Creating Genes table
> Appending Probes
> Found 0 Probe Accessions
> Appending Gene Info
> Found 49221 Gene Names
> Found 49221 Gene Symbols
> Appending Chromosomes
> Appending Cytogenetic Locations
> Appending Omim
> Appending RefSeq
> Appending Pubmed
> Appending Unigene
> Appending ChrLengths
> Appending 3 GO tables
> Appending 3 GO ALL tables
> Appending KEGG
> Appending EC
> Appending Chromosome Locations
> Appending Pfam
> Appending Prosite
> Appending Alias
> Appending Ensembl
> Appending Metadata 
> 
> 
> Creating package in ./hgu95a-e2.db
> 
> > library("hgu95a-e2.db", lib.loc = getwd())
> Error in library("hgu95a-e2.db", lib.loc = getwd()) : 
>   'hgu95a-e2.db' is not a valid package -- installed < 2.0.0?
> 
> Thanks,
> Fraser
> 
> -----Original Message-----
> From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean
Davis
> Sent: Thursday, October 30, 2008 4:19 PM
> To: Sim, Fraser
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Annotation packages
> 
> On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser
> <Fraser_Sim at urmc.rochester.edu> wrote:
> > Hi-
> >
> >
> >
> > I have a quick question relating to the use of annotation packages
in
> > Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C,
D, E
> > chips. I have performed RMA and generated expression data for each
chip
> > type individually and then used rbind to make a single matrix with
all
> > the data. I can use limma just fine to then perform differential
gene
> > analysis.
> >
> >
> >
> > I would like to use additional functions such as GO Hyper G testing
but
> > I couldn't find an annotation package that combined all 5 chips. How
> > would I go about generating a new annotation package that combined
the
> > five individual annotation packages? Or how should I approach this
> > problem?
> 
> You can always build your own annotation package.  The documentation
> is in the AnnotationDbi package.  In particular, see the SQLForge
> vignette.
> 
> Sean
> 
> > SessionInfo:
> >
> >
> >
> > R version 2.7.0 (2008-04-22)
> >
> > i386-pc-mingw32
> >
> >
> >
> > locale:
> >
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> >
> >
> > attached base packages:
> >
> > [1] splines   stats     graphics  grDevices datasets  utils
tools
> > methods   base
> >
> >
> >
> > other attached packages:
> >
> >  [1] hgu95av2.db_2.2.0    bioDist_1.12.0       gplots_2.6.0
> > gdata_2.4.2          gtools_2.5.0
> >
> >  [6] RColorBrewer_1.0-2   RODBC_1.2-3          affycoretools_1.12.0
> > annaffy_1.12.1       KEGG.db_2.2.0
> >
> > [11] gcrma_2.12.1         matchprobes_1.12.0   biomaRt_1.14.0
> > RCurl_0.9-3          GOstats_2.6.0
> >
> > [16] Category_2.6.0       RBGL_1.16.0          annotate_1.18.0
> > xtable_1.5-2         GO.db_2.2.0
> >
> > [21] AnnotationDbi_1.2.2  RSQLite_0.6-9        DBI_0.2-4
> > graph_1.18.1         limma_2.14.5
> >
> > [26] genefilter_1.20.0    survival_2.34-1      affy_1.18.2
> > preprocessCore_1.2.0 affyio_1.8.0
> >
> > [31] Biobase_2.0.1
> >
> >
> >
> > loaded via a namespace (and not attached):
> >
> > [1] cluster_1.11.10 XML_1.94-0.1
> >
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor