CanFam2 data RNAseq samples and GenomicRanges

[biofreak]

hi All,
I am processing RNAseq samples for canFam2. I used the following commands from GenomicRanges package that gives me only 1218 genes. (because by default refGene for canFam2 retains only known genes.)

txdb <- makeTranscriptDbFromUCSC(genome = "canFam2", tablename = "refGene")
TranscriptDb object:
| Db type: TranscriptDb
| Data source: UCSC
| Genome: canFam2
| UCSC Table: refGene
| Type of Gene ID: Entrez Gene ID
| Full dataset: yes
| transcript_nrow: 1218
| exon_nrow: 11256
| cds_nrow: 10922
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2011-08-08 12:56:52 -0400 (Mon, 08 Aug 2011)
| GenomicFeatures version at creation time: 1.4.2
| RSQLite version at creation time: 0.9-4
| DBSCHEMAVERSION: 1.0

To get all the genes, I changed the table name to "xenoRefGene" but that does not fetch the "gene Ids". Also, the number of transcripts (229403) looks abnormally large.

TranscriptDb object:
| Db type: TranscriptDb
| Data source: UCSC
| Genome: canFam2
| UCSC Table: xenoRefGene
| Type of Gene ID: no gene ids
| Full dataset: yes
| transcript_nrow: 229403
| exon_nrow: 1110585
| cds_nrow: 747878
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2011-08-08 12:51:29 -0400 (Mon, 08 Aug 2011)
| GenomicFeatures version at creation time: 1.4.2
| RSQLite version at creation time: 0.9-4
| DBSCHEMAVERSION: 1.0


please help.