Hi everyone in list, I tried to use limma2annaffy function in "affycoretools" package, but got the message as following, can anybody tell me how to solve it? Thank you in advance!!! Hui-Yi Do you want to accept or change these values? [ a/c ]a Loading required package: yeast2 ******* Deprecation warning *******: The package 'yeast2' is deprecated and will not be supported in the future. Instead we strongly reccomend that you should start using the 'yeast2.db' package. We hope you will enjoy these new packages. If you still have questions, you can search (http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list (http://bioconductor.org/docs/mailList.html). Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : could not find function "yeast2_dbconn" In addition: Warning message: In chkPkgs(chip) : The yeast2 package does not appear to contain annotation data. ##### R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] yeast2_2.2.0 affycoretools_1.12.1 annaffy_1.12.1 [4] KEGG.db_2.2.0 gcrma_2.12.1 matchprobes_1.12.1 [7] biomaRt_1.14.1 RCurl_0.9-3 GOstats_2.6.0 [10] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 [13] xtable_1.5-3 GO.db_2.2.0 AnnotationDbi_1.2.2 [16] RSQLite_0.7-0 DBI_0.2-4 graph_1.18.1 [19] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 [22] Heatplus_1.10.0 RColorBrewer_1.0-2 genefilter_1.20.0 [25] survival_2.34-1 yeast2cdf_2.2.0 limma_2.14.6 [28] affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 [31] Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1 Thanks again!! Hui-Yi [[alternative HTML version deleted]]

Hi Hui-Yi, Hui-Yi Chu wrote: > Hi everyone in list, > > I tried to use limma2annaffy function in "affycoretools" package, but got > the message as following, can anybody tell me how to solve it? Thank you in > advance!!! Yes. For now, let's say your ExpressionSet is called 'eset'. annotation(eset) <- "yeast2.db" Then run the analysis as usual. Best, Jim > > Hui-Yi > > > > Do you want to accept or change these values? [ a/c ]a > Loading required package: yeast2 > > ******* Deprecation warning *******: > > The package 'yeast2' is deprecated and will not be supported in the future. > > Instead we strongly reccomend that you should start using the 'yeast2.db' > package. > > We hope you will enjoy these new packages. If you still have questions, you > can search > (http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask > the mailing list > (http://bioconductor.org/docs/mailList.html). > > > Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : > could not find function "yeast2_dbconn" > In addition: Warning message: > In chkPkgs(chip) : > The yeast2 package does not appear to contain annotation data. > > > > ##### > R version 2.7.2 (2008-08-25) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] yeast2_2.2.0 affycoretools_1.12.1 annaffy_1.12.1 > [4] KEGG.db_2.2.0 gcrma_2.12.1 matchprobes_1.12.1 > [7] biomaRt_1.14.1 RCurl_0.9-3 GOstats_2.6.0 > [10] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > [13] xtable_1.5-3 GO.db_2.2.0 AnnotationDbi_1.2.2 > [16] RSQLite_0.7-0 DBI_0.2-4 graph_1.18.1 > [19] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 > [22] Heatplus_1.10.0 RColorBrewer_1.0-2 genefilter_1.20.0 > [25] survival_2.34-1 yeast2cdf_2.2.0 limma_2.14.6 > [28] affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 > [31] Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 XML_1.94-0.1 > > > Thanks again!! > Hui-Yi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662