[BioC] Minimum expression threshold?

[w.huber at dkfz-heidelberg.de]

Hi Bob,

> This shows the minimum expression value is 3.083 - but the tissue I'm
> using cannot be expressing all of these genes (I'm hybridizing to the
> U133A chip).
>  * What exactly is the expression value that RMA returns?  I know it is
> log2 transformed, but I don't understand what it corresponds to.

Before the log2 transformation, there is a background correction, and what
that does is to "push up" or bias the data a little bit upwards, to make
sure that the data are all positive, even for unexpressed genes. This has
the advantage of making the variance of the log2 (-ratios) more stable.

> * Should RMA only be used for comparative studies?
> What if someone wanted to create a database of all genes expressed in
> tissue X? (not that I'm doing this, but what if?)

How do you define "expressed in tissue X"? How many copies of the
transcript per cell, in what fraction of cells among the population of
cells?

Also, there is always some kind of background signal, even if very small,
from unspecific hybridisation and the like, so that at the lower end of
the intensity spectrum it is probably is not possible to find a threshold
that yields both a low false positive and high true positive rate.

Also, a more sensitive criterion to decide whether a gene is actually
expressed or not may be to look for correlation of its expression values
with those of other genes or phenotypic variables. (If it is not
expressed, the "noise" should show no such correlations.)

Best regards
  Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/mga/whuber