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

Mon Aug 3 22:12:46 CEST 2009

Hi Marco,

both bugs are fixed in version 1.19.3 of siggenes which should be available in the devel section of Bioconductor soon, as I have just committed this version.

Best,
Holger

-------- Original-Nachricht --------
> Datum: Mon, 3 Aug 2009 16:41:32 +0200
> Von: "Manca Marco (PATH)" <m.manca at path.unimaas.nl>
> An: Holger Schwender <holger.schw at gmx.de>, "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Betreff: R: Minor problem with siggenes\'s command sam2excel when entrez=TRUE

> 
> 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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