Hi Paul, I think you're confusing two functions: Have a look at the man page for xmapGene()... It (and the related functions xmapTranscript(), xmapExon() and xmaProbeset()) simply opens up a browser window on xmap, located at the gene, (or transcript, etc...) specified. It doesn't do anything with the expression data and simply takes one parameter, the gene id. The error you're getting is R complaining that you're calling xmapGene with lots of unused arguments (including eset). The function xmapBridge() is what you want to use to write out expression data for the XMapBridge. It doesn't expect the parameter 'use.bridge', though... This should work, however!: xmapBridge(<my gene="" id="">,eset=affy. rma,gps=list(A=1:3,B=4:6), type="fc",overwrite=FALSE) Crispin On 5/2/08 18:01, "Vincent Carey 525-2265" <stvjc at="" channing.harvard.edu=""> wrote: > >> dear all, >> >> I am trying to plot different gene/transcript/exon expressions from exon >> affymetrix chips by using the function 'xmapGene' or 'xmapBridge' >> (package exonmap). but when I start these functions I get an error >> message, that I have to use <s4 object="" of="" class="" "expressionset"=""> for >> value 'eset'. I used this code: >> >>> raw.data = read.exon() >>> raw.data at cdfName = "exon.pmcdf" >>> affy.rma = rma(raw.data) >> Background correcting >> Normalizing >> Calculating Expression >>> xmapDatabase("Human") >> done. >>> xmapGene("ENSG00000128655", *eset=affy.rma*, >> use.bridge=TRUE,gps=list(A=1:3,B=4:6),type="fc",overwrite=FALSE) >> Error in xmapGene("ENSG00000128655", *eset = affy.rma*, use.bridge = >> TRUE, : >> unused argument(s) (*eset = <s4 object="" of="" class="" "expressionset"="">*, >> use.bridge = TRUE, gps = list(A = 1:3, B = 4:8), type = "fc", overwrite >> = FALSE) >> >> I thought that the function rma() results in an S4 object of the class >> "exprSet", isn't it??? and is "exprSet"the same like "ExpressionSet"? >> Is there any chance to get an S4 object of class "ExpressionSet??? > > Please provide a sessionInfo() result to tell us the versions > of R and the various packages you are using. > > "exprSet" is the name of a legacy class that is not to be used in > current applications. There may be software on your system that > generates "exprSet" instances but it should be updated. > > "ExpressionSet" is the name of the class that replaces "exprSet". > > In the current version of exonmap, xmapGene has a single parameter "x". > So your call with numerous parameters shown above (hard to decipher) > may not be valid. > > The information transmitted in this electronic communica...{{dropped:9}} > > _______________________________________________ > 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 -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}

dear all, the function xmapBridge() (package exonmap) worked fine until i did a reboot. now always comes this mysql error message: > xmapBridge("ENSG00000115252",eset=rma.affy,gps=list(A=1:3,B=4:8),type= "fc") Fehler in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: Unknown database 'homo_sapiens_core_47_36i') when i login to mysql the database with all tables is there. here my session info: > sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE .UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] exon.pmcdf_1.1 exonmap_1.4.1 plier_1.8.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.14.05 gcrma_2.10.0 matchprobes_1.10.0 [10] genefilter_1.16.0 survival_2.32 affy_1.16.0 [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.2 loaded via a namespace (and not attached): [1] annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-15 [4] RSQLite_0.6-4 have someone an idea??? thanks paul