[BioC] Annotation packages

Fri Oct 31 16:21:13 CET 2008

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.

Thanks,
Fraser

-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
Sent: Thursday, October 30, 2008 5:51 PM
To: Sim, Fraser
Cc: Sean Davis; bioconductor at 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 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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>>     
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