Question: Question about filtering genes when using siggenes
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gravatar for Manca Marco PATH
9.8 years ago by
Manca Marco PATH200 wrote:
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: luned? 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: mercoled? 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_Netherland s.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 > > -- > Neu: GMX Doppel-FLAT mit Internet-Flatrate + Telefon-Flatrate > f?r nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02 -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
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