[BioC] Question about filtering genes when using siggenes
Manca Marco (PATH)
m.manca at path.unimaas.nl
Fri Aug 7 15:40:10 CEST 2009
Dear Holger,
good afternoon.
I was wondering whether there is a parameter that I can add directly to my siggenes command string to exclude or include a specific set of genes from my ExpressionSet from/into my analysis (as instance according to the expression level or the Gene Ontology, assuming I have included these data in my ExpressionSet or that I have the output file of a prior genefilter operation)?
Thank you in advance for your kind attention. My best regards,
Marco
--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht
E-mail: m.manca at path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
________________________________________
Da: Holger Schwender [holger.schw at gmx.de]
Inviato: lunedì 3 agosto 2009 22.12
A: Manca Marco (PATH); bioconductor at stat.math.ethz.ch
Oggetto: Re: R: Minor problem with siggenes's command sam2excel when entrez=TRUE
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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