Off topic:low overlap using hugene10stprobeset

Question

[Palgrave]

I am trying to map my affy data IDs using the package hugene10stprobeset.db, but I only get an overlap for about 200 gene names. Am I using the wrong probeset?

mydata:

> mRNA.affy[,1:5][1:5,]
   ID_REF GSM409113 GSM409114 GSM409115 GSM409116
1 7892501  2.868901  8.338831  7.382292  8.302262
2 7892502  3.623899  6.205984  3.615587  4.621667
3 7892503  2.272131  2.635364  2.007095  2.761859
4 7892504  9.542684 10.542620 10.020340 10.194740
5 7892505  2.533892  3.791065  2.439405  2.410347

> dim(mRNA.affy)
[1] 33298    66




  > head(genesym.probeid)
  probe_id      ensembl_id
1  8039749 ENSG00000121410
2  8039750 ENSG00000121410
3  8039751 ENSG00000121410
4  8039752 ENSG00000121410
5  8039753 ENSG00000121410
6  8039754 ENSG00000121410