Thanks Marc

Sorry for the late reply, I was away for a week. I did use SQLForge to make a (AnnotationDbi) custom  package that I called GGal.db. It works for all I need, like oligo, limma etc, but when I tried to run goProfyles package with GGal.db it was asking for the object "GGal.dbENTREZID' not found"  Because it named the object starting with GGal.db I assumed that the object should be in the database, and since it was not there, I again assumed I should find a way to add it to db. I know it is looking for a file with 2 columns, my platform gene ID vs ENTREZ ID. I thought if I add this table to the sqlite database maybe it would work??? I was probably wrong. Then I thought that I should make an object in R (not in the database) and call it GGal.dbENTREZID. I tried this:
>GGal.dbENTREZID=read.table("GGal.dbENTREZID.txt", header=TRUE, sep="\t")
> head(GGal.dbENTREZID)
           ID ENTREZID
1 CLIGG_02786   373854
2   RIGG10718   373854
3 CLIGG_03262   373886
4   RIGG10181   373886
5   RIGG10182   373886
6 CLIGG_01647   373887

Then the goProfiles did not ask for the object GGal.dbENTREZID but gave me an error:
Error in mget(probeslist, env = myenvir, ifnotfound = NA) :
  second argument must be an environment

As usual I tried to google out what this means with no success. I assume I should use something other than read.table to make an object but I could not find instructions in the package. I only know basic R and the packages I need to use, I can use any help or advice in how to proceed.

Thanks
Dana

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