The NF and M are both related to the reference genes, but in a
completely different way. The M value must be interpreted as a
quality parameter for the stability of the selected reference genes.
The NF (normalization factor) values are a measure to correct for the
differences in the amount of total input DNA between samples. Your
results indicate that the amount of DNA in your two groups differ by
about a factor 10. Although normalization is performed to correct for
this difference, it is still advisible to minimize these differences
in future experiments.

Jan

--- In qBase@yahoogroups.com, "o_o_phil" <o_o_phil@...> wrote:
>
> Hello,
>
> I am concerned with difference among NFs for our experimental setup of
> two groups of tissue pools. The NFs are near 0.3 in one group, and 2.5
> in the other. In this setup we used 7 references genes, and the
> overall M is 0.650.
>
> Using geNorm we selected the two most stable genes among the 7,
> obtaining a M of 0.169 with the two. However, the NF histogram looks
> about the same as with the 7 ref genes: near 0.3 for one tissue group
> and near 2.5 for the other group. What's the difference between M and
> NF histogram when assessing ref genes stability?
>
> How can we interpret the final CNRQ histogram for our genes of
> interest based on those results about the reference genes? Is this
> strong difference among NFs disrupt the normalization, or on the other
> hand removes the expression bias detected among the reference genes?
> Can we make fold difference assumption in our genes of interest
> knowing this difference between NFs?
>
> thanks in advance for any insight you can give me!
>
> Phil
>