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










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