Answers inserted into the text.

--- In qBase@yahoogroups.com, Adrian Marius Peres Bota
<aperesbota@...> wrote:


Dear Jo

Would you please have a look to the questions bellow that rose during
an internal meeting?

1) What is/are the advantage(s) to use the mean Ct for
calculating the relative quantities (qBase) instead of the min Ct
(GeNorm)?

==> As explained in the qBase paper, the choice of the reference Ct
(mean or min or ...) does not affect your results. When taking into
account the error on the amplification efficiency the overall error
can be minimized by using the mean Ct as the reference Ct.

2) Knowing such different approach (qBase vs. GeNorm), why is
it necessary to estimate firstly the ref. genes in GeNorm and then use
them in qBase if we are not applying the same method for calculating
the relative quantities.

==> geNorm allows you to select the best set of reference genes in a
pilot experiment. By calculating the same quality parameter (geNorm M
value), qBase allows you to verify wether your reference genes are
still stable in your actual experiment. Therefore geNorm and qBase
can be considered complimentary: they perform validation and quality
control respectively.

3) Would it be possible to implement the GeNorm approach in
qBase allowing then comparisons?

==> The development of qBase has been terminated. Biogazelle will
however release a professional version (qBasePlus) which will
integrate geNorm in the future.

Looking forward to your answer.

Best regards,
Adrian