Unidentified genes in a microarray gene expression dataset

Question

[Shaurya Jauhari]

Is it wise to discard non-annotated genes in the microarray gene expression dataset?

Answer 1

[Charles Warden]

Please provide more detailed information with your question.

If you are using an Affy array, you can use NetAffx to get the probe sequences. While I could consider the probes for annotated genes to generally be more reliable (since, depending upon your array design, those unannotated probes are often intended to be control probes), you can BLAT the associated genome sequence to see if they overlap some newly discovered gene.