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_M ONETARY=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

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 -- f?r nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02