Hi Sean-

 

Thanks. I guess what’s not very clear is how to do that in the documentation. Here’s how I did it in case other new users need more help.

 

Install RTools from http://www.murdoch-sutherland.com/Rtools/

 

Open a cmd prompt (Start -> Run -> cmd.exe)

Go to your program files folder and find the R installation folder. Go to the bin directory.

Type Rcmd.exe INSTALL pkgname

(Note: remember to use escape the backslash as in “\\” as otherwise R will parse the pkgname path incorrectly.)

 

Hope that helps. My new annotation package installed just fine. I’ll use this technique to help out another lab member working with a custom eArray.

 

Cheers,

Fraser

 

 

From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis
Sent: Friday, October 31, 2008 11:25 AM
To: Sim, Fraser
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] Annotation packages

 

 

On Fri, Oct 31, 2008 at 11:21 AM, Sim, Fraser <Fraser_Sim@urmc.rochester.edu> wrote:

Hi Marc,

My sessionInfo is at the end of the original email.

How do I use R CMD INSTALL? I am on WindowsXP and it looks like
something I'd need Linux to use?


You'll need to install RTools.  See the R-for-windows FAQ for details.

Sean
 

	
	-----Original Message-----
	From: Marc Carlson [mailto:mcarlson@fhcrc.org]
	Sent: Thursday, October 30, 2008 5:51 PM
	To: Sim, Fraser
	Cc: Sean Davis; bioconductor@stat.math.ethz.ch
	Subject: Re: [BioC] Annotation packages
	
	Hi Fraser,
	
	Did you R CMD INSTALL the package that you made?  SQLForge will produce
	the source code for the package you want, but you need to then use R to
	build or install it.  You cannot just call library to try and load it
	without even leaving the session which is what your post seems to
	suggest.  Also can you show us your sessionInfo()?
	
	
	 Marc
	
	
	
	
	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@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean
	Davis
	> Sent: Thursday, October 30, 2008 4:19 PM
	> To: Sim, Fraser
	> Cc: bioconductor@stat.math.ethz.ch
	> Subject: Re: [BioC] Annotation packages
	>
	> On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser
	> <Fraser_Sim@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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	>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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	http://news.gmane.org/gmane.science.biology.informatics.conductor
	>>
	>>
	> _______________________________________________
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	> https://stat.ethz.ch/mailman/listinfo/bioconductor
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	>
	>
	
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