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

[Manca Marco (PATH)]

Dear Holger,

thank you for your kind reply.

I would like to ask for your suggestions once more: I am trying an EBAM analysis on the same datasets as last time (the GSE9820 from Gene Expression Omnibus) and I encounter the following error right at my first step
> find.out <- find.a0(gse, gse$source_name_ch1, rand = 123, gene.names = fData(gse)$GB_ACC)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "annotation", for signature "matrix"

the same happens if I omit the gene.names

I have tried to browse the vignette and the reference manual (http://www.bioconductor.org/packages/2.4/bioc/manuals/siggenes/man/siggenes.pdf) but I am unable to get a clue at what it is asking annotation for and how can I adapt to this request.

Could you suggest me how to proceed?

Thank you in advance for your attention and support.

My best regards,
Marco


--
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
________________________________________
Da: Holger Schwender [holger.schw at gmx.de]
Inviato: mercoledì 29 luglio 2009 16.31
A: Manca Marco (PATH); bioconductor at stat.math.ethz.ch
Oggetto: Re: Minor problem with siggenes's command sam2excel when entrez=TRUE

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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