[BioC] Annotation packages

[Sim, Fraser]

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]]
>
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