[BioC] Minor problem with siggenes's command sam2excel when entrez=TRUE

[Holger Schwender]

Hi Marco,

I will fix this in a few days. In the meanwhile, you can load your annotation package first and then call sam2excel, and it actually should work.

Best,
Holger


-------- Original-Nachricht --------
> Datum: Wed, 29 Jul 2009 16:23:46 +0200
> Von: "Manca Marco (PATH)" <m.manca at path.unimaas.nl>
> An: bioconductor mailing list <bioconductor at stat.math.ethz.ch>, "Holger Schwender" <holger.schw at gmx.de>
> Betreff: Minor problem with siggenes\'s command sam2excel when entrez=TRUE

> 
> Dear Holger and dear Bioconductors,
> 
> I am using siggenes to perform SAM on the dataset gse9820 (mainly
> replicating the elaboration described by the authors of the object). It works
> perfectly but when I am exporting my SAM output of interest to a .csv files it
> gives me an error message if I ask to add Entrez links to the output (entrez
> = TRUE). It works just fine if I omit this requeste:
> 
> > sam2excel(sam.out1, 0.4, "control_patient_diffExpr12.csv",
> excel.version=2, n.digits = 5, entrez = TRUE, what = "both", quote = FALSE)
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Error: getAnnMap: GPL6255.db package not attached and load is FALSE
> Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
> ifnotfound = NA) : 
>   error in evaluating the argument 'envir' in selecting a method for
> function 'mget'
> 
> 
> whilst
> 
> 
> > sam2excel(sam.out1, 0.4, "control_patient_diffExpr.csv",
> excel.version=2, n.digits = 5, what = "both", quote = FALSE)
> Output is stored in control_patient_diffExpr.csv 
> 
> 
> This is not a major issue, since I have already the Entrez ID (
> NM_######.#)  instead of the Illumina ID on the output files:
> > sam.out1 <- sam(gse, gse$characteristics_ch1, gene.names =
> fData(gse)$GB_ACC)
> 
> Yet I wonder if there's a way to make it work. I have tried preserving the
> Illumina ID (basically omitting the #gene.names = fData(gse)$GB_ACC#
> option from the sam command) along my analysis and then associating the sam
> output to an annotation database (through the #chip = "chipID"# option) in
> sam2excel but it didn't work, neither with "lluminaHumanv2BeadID" nor with
> "lumiHumanAll".
> 
> Where am I doing wrong? Thank you in advance.
> 
> Best regards, Marco
> 
> 
> -----By the way, the following is my session info, just in case------
> > sessionInfo()
> R version 2.9.0 (2009-04-17) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MONETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
> 
> attached base packages:
> [1] splines   stats     graphics  grDevices datasets  utils     methods  
> [8] base     
> 
> other attached packages:
>  [1] annotate_1.22.0     AnnotationDbi_1.6.1 GEOquery_2.8.0     
>  [4] RCurl_0.98-1        bitops_1.0-4.1      affy_1.22.0        
>  [7] siggenes_1.18.0     multtest_2.1.1      Biobase_2.4.1      
> [10] rcom_2.2-1          rscproxy_1.3-1     
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0        DBI_0.2-4            MASS_7.2-47         
> [4] preprocessCore_1.6.0 RSQLite_0.7-1        survival_2.35-4     
> [7] tools_2.9.0          xtable_1.5-5  
> 
> --------END-------
> 
> -- 
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
> E-mail: m.manca at path.unimaas.nl
> Mobile: +31626441205
> Twitter: @markomanka

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