I am trying to make annotation package for my array platform using AnnotationDbi package. I prepared txt file that links customID and unigene. The table I am trying to import here has only 2 columns; one is gene id (CLIGG_00001) and the other is unigene id (Gga.1). I tried all I could google out and many as.character or bimap options...Here is the R output: > setwd("/home/dana/MICROARRAY/Results/Pancreas") > dir() [1] "GGal_ID_UG.txt" > library(AnnotationDbi) > GGal_ID=read.table(as.character("GGal_ID_UG.txt", sep = "\t", header = FALSE, as.is = TRUE)) > mode(GGal_ID) [1] "list" > class(GGal_ID) [1] "data.frame" > # > # > ls() [1] "GGal_ID" > head (GGal_ID) V1 V2 1 CLIGG_00001 Gga.1 2 CLIGG_00002 Gga.3 3 CLIGG_00003 Gga.4 4 CLIGG_00004 Gga.5 5 CLIGG_00005 Gga.6 6 CLIGG_00006 Gga.6 > available.db0pkgs() [1] "anopheles.db0" "arabidopsis.db0" "bovine.db0" "canine.db0" [5] "chicken.db0" "chimp.db0" "ecoliK12.db0" "ecoliSakai.db0" [9] "fly.db0" "human.db0" "malaria.db0" "mouse.db0" [13] "pig.db0" "rat.db0" "rhesus.db0" "worm.db0" [17] "xenopus.db0" "yeast.db0" "zebrafish.db0" > library(chicken.db0) > myMeta = c("DBSCHEMA"="CHICKENCHIP_DB", "ORGANISM"="Gallus gallus", "SPECIES"="Chicken", "MANUFACTURER"="NimbleGen", "CHIPNAME"="090716_Ggal_RM_EXP", "MANUFACTURERURL"="http://www.roche.com") > populateDB("CHICKENCHIP_DB", affy = FALSE, prefix = "GGal", fileName = GGal_ID, metaDataSrc = myMeta, baseMapType = "ug") Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection How to import my table (GGal_ID_UG.txt) as a character string or connection? Is there a simple code to get from my own txt file to a annotation package? Thanks in advance for posting a reply. Dana [[alternative HTML version deleted]]

Hi Dana, First of all let me say that it fills me with joy to see someone finally making use of the "chicken.db0" package. Next, I think the error you have is trying to indicate that you need to pass "GGal_ID_UG.txt" in to the file parameter. Like this: populateDB("CHICKENCHIP_DB", affy = FALSE, prefix = "GGal", fileName = "GGal_ID_UG.txt", metaDataSrc = myMeta, baseMapType = "ug") Let me know if you have other problems that crop up. Marc On 03/17/2011 08:33 PM, Dana.Stanley at csiro.au wrote: > I am trying to make annotation package for my array platform using AnnotationDbi package. I prepared txt file that links customID and unigene. The table I am trying to import here has only 2 columns; one is gene id (CLIGG_00001) and the other is unigene id (Gga.1). I tried all I could google out and many as.character or bimap options...Here is the R output: > > > > > >> setwd("/home/dana/MICROARRAY/Results/Pancreas") >> dir() > [1] "GGal_ID_UG.txt" > > > >> library(AnnotationDbi) > > >> GGal_ID=read.table(as.character("GGal_ID_UG.txt", sep = "\t", header = FALSE, as.is = TRUE)) > > >> mode(GGal_ID) > [1] "list" > >> class(GGal_ID) > [1] "data.frame" > >> # >> # >> ls() > [1] "GGal_ID" > > > >> head (GGal_ID) > V1 V2 > > 1 CLIGG_00001 Gga.1 > > 2 CLIGG_00002 Gga.3 > > 3 CLIGG_00003 Gga.4 > > 4 CLIGG_00004 Gga.5 > > 5 CLIGG_00005 Gga.6 > > 6 CLIGG_00006 Gga.6 > > > >> available.db0pkgs() > [1] "anopheles.db0" "arabidopsis.db0" "bovine.db0" "canine.db0" > > [5] "chicken.db0" "chimp.db0" "ecoliK12.db0" "ecoliSakai.db0" > > [9] "fly.db0" "human.db0" "malaria.db0" "mouse.db0" > > [13] "pig.db0" "rat.db0" "rhesus.db0" "worm.db0" > > [17] "xenopus.db0" "yeast.db0" "zebrafish.db0" > > > >> library(chicken.db0) > > >> myMeta = c("DBSCHEMA"="CHICKENCHIP_DB", "ORGANISM"="Gallus gallus", "SPECIES"="Chicken", "MANUFACTURER"="NimbleGen", "CHIPNAME"="090716_Ggal_RM_EXP", "MANUFACTURERURL"="http://www.roche.com") > > >> populateDB("CHICKENCHIP_DB", affy = FALSE, prefix = "GGal", fileName = GGal_ID, metaDataSrc = myMeta, baseMapType = "ug") > Error in read.table(file = file, header = header, sep = sep, quote = quote, : > > 'file' must be a character string or connection > > > How to import my table (GGal_ID_UG.txt) as a character string or connection? Is there a simple code to get from my own txt file to a annotation package? > > Thanks in advance for posting a reply. > > Dana > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

THANKS MARK!!!! I have my package up and running! xoxoxo [[alternative HTML version deleted]]