Housekeeping Genes in Lymphoma

[kicka11]

A seemingly very simple question, but not one that I can find the answer to from experts or the literature.

I am using NanoString to look at pathway signalling in aggressive B cell Non-Hodgkin Lymphoma.

Our preliminary data showed very variable expression of the included HKs (ACTB, TUBB, GAPDH) so in future iterations we are going to use TBF which has been validated in one or two papers.

Any other ideas? Does anyone have experience regarding this?
I thought we could look through old affymetrix data for consistent expression of certain genes but our biostats person does not seem keen on this approach.

Any ideas very welcome.

[thomasblomquist]

Genorm is often used in Real-Time experiments.

The basic idea is that you need to determine a geometric mean for your expression data, and normalize to that. Simply, if you have 50 or even better, 100's of genes, determine a geometric mean of the population of expression, and normalize to that median expression measurement.

HK genes is the way we use to normalize data when we couldn't interrogate more than a few genes cost-effectively.

-Tom