Comparing Expression Of Two Genes With The Same Microarray

Question

[pmoney1]

Hi,

I'm wondering if anyone is aware of any method by which it is possible to compare the expression of two genes within the same microarray sample? I know that normally you can't (accurately) compare expression of genes within the same sample because of hybridization differences etc. so this may be a long shot....

Thanks!

Answer 1

[Chris Evelo]

I think you already answer your own question. There are indeed a lot of reasons (which differ by exact technology used) that influence the relationship between abundance on a gene product and the binding to the microarray. There are ways to at least partly overcome that. For instance GCRMA normalisation on Affymetrix arrays tries to overcome differences caused by differences in GC content per probe (that doesn't fully work though), usage of thermodynamically stabilized probes that also want to normalize binding and melt energies (used by Nimblegen and some miRNA array manufacturers) or simply using probes of the same length. The more your sample treatment and technology used are able to decrease such differences the more the basic assumption will hold that higher binding is likely caused by higher abundance. Although it will not become linear that is in the end what you will use as an estimation if you have to.