Dear Kasper, sorry I read the vignette but missed the point related to the fact that ExpData object is essentially just a pointer. Your example: eData<- ExpData(dbFilename = "gilli.db", tablename = "gf11") makes every think clear to me. Many thanks again. Raffaele P.S. Genominator is really a nice piece of software I nicely managed to create the table to be used in edgeR in less than an hour for a project of Illumina ncRNA (97 milion mapped reads on 14 samples) on my portable computer. 24/05/2010 15:31, Kasper Daniel Hansen ha scritto: > Just to be clear. In your case you would create the pointer to the > table in the database by > > eData<- ExpData(dbFilename = "gilli.db", tablename = "gf11") > > Kasper > > On Mon, May 24, 2010 at 9:30 AM, Kasper Daniel Hansen > <kasperdanielhansen at="" gmail.com=""> wrote: > >> Hi Raffaele >> >> As described in the user guide: you should not save the ExpData object >> as it contains an active connection. >> >> The rExpData object is essentially just a pointe to a table in a >> database, so it takes no time to instantiate; hence we see no real >> need for saving it. We might be able to figure out a way to do so, >> but we estimated it would take too much time for the little benefit it >> would yield. >> >> Kasper >> >> On Mon, May 24, 2010 at 5:58 AM, rcaloger<raffaele.calogero at="" unito.it=""> wrote: >> >>> Hi, >>> I am loading NGS data in Genominator package. >>> Everything is going smoothly in data loading. >>> >>>> df<- read.table("s_5_2.ctrl11.txt.25.out.bed", sep="\t", as.is=T) >>>> names(df)<- c("chr", "strand", "location") >>>> df[1:3,] >>>> >>> chr strand location >>> 1 3 -1 121374316 >>> 2 3 -1 121374316 >>> 3 3 -1 121374316 >>> >>> >>>> eDataRaw<- importToExpData(df, "gilli.db", tablename = "gf11") >>>> eDataRaw >>>> >>> table: gf11 >>> database file: H:\data\gilli\ncRNA\gilli.db >>> index columns: chr location strand >>> mode: w >>> schema: >>> chr location strand >>> "INTEGER" "INTEGER" "INTEGER" >>> >>> However, I could not find a specific function to save the Genominator object >>> and to load it again. >>> I trayied with save() >>> save(eDataRaw,file="eDataRaw.rda") >>> but if I load it again I get an error : >>> >>>> load("eDataRaw.rda") >>>> eDataRaw >>>> >>> table: gf11 >>> database file: H:\data\gilli\ncRNA\gilli.db >>> index columns: chr location strand >>> mode: w >>> schema: >>> Error in get(.makeDBConnectionName(.Object), .pool) : >>> object "H:\data\gilli\ncRNA\gilli.db___w" non found >>> Error in dbGetQuery(con, q) : >>> error in evaluating the argument 'conn' in selecting a method for function >>> 'dbGetQuery' >>> >>> Does anybody know how to save a ExpData-class object? >>> >>> >>>> sessionInfo() >>>> >>> R version 2.11.0 (2010-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 >>> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C >>> [5] LC_TIME=Italian_Italy.1252 >>> >>> attached base packages: >>> [1] grid tools tcltk stats graphics grDevices utils >>> [8] datasets methods base >>> >>> other attached packages: >>> [1] Genominator_1.2.0 GenomeGraphs_1.8.0 biomaRt_2.4.0 >>> [4] oneChannelGUI_1.15.2 edgeR_1.6.5 IRanges_1.6.0 >>> [7] preprocessCore_1.10.0 GOstats_2.14.0 RSQLite_0.8-4 >>> [10] DBI_0.2-5 graph_1.26.0 Category_2.14.0 >>> [13] AnnotationDbi_1.10.0 tkWidgets_1.26.0 DynDoc_1.26.0 >>> [16] widgetTools_1.26.0 affylmGUI_1.22.0 affyio_1.16.0 >>> [19] affy_1.26.0 limma_3.4.0 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.26.0 genefilter_1.30.0 GO.db_2.4.1 GSEABase_1.10.0 >>> [5] RBGL_1.24.0 RCurl_1.3-1 splines_2.11.0 survival_2.35-8 >>> [9] XML_2.8-1 xtable_1.5-6 >>> >>>> >>> cheers >>> Raffaele >>> >>> -- >>> >>> ---------------------------------------- >>> Prof. Raffaele A. Calogero >>> Bioinformatics and Genomics Unit >>> Dipartimento di Scienze Cliniche e Biologiche >>> c/o Az. Ospedaliera S. Luigi >>> Regione Gonzole 10, Orbassano >>> 10043 Torino >>> tel. ++39 0116705417 >>> Lab. ++39 0116705408 >>> Fax ++39 0119038639 >>> Mobile ++39 3333827080 >>> email: raffaele.calogero at unito.it >>> raffaele[dot]calogero[at]gmail[dot]com >>> www: http://www.bioinformatica.unito.it >>> Info: http://publicationslist.org/raffaele.calogero >>> >>> _______________________________________________ >>> 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 >>> >>> >> > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero