First step is the calculation of efficiency, denoted by lets say $E_{gene}$. See this post for calculation of primer efficiency.

So the fold change for that gene will be calculated by $E_{gene}^{-\Delta Ct_{gene}}$

Where:

$\Delta Ct  = Ct^{treated} -Ct^{control}$

But these Ct values are not normalized. For normalization, you take some reference gene which need not be a housekeeping gene. Reference gene should chosen such that it is not affected by the treatment. In some cases usual housekeeping genes can also get affected for e.g. in treatments affecting cell cycle or differentiation. In such cases you should use a spike-in (an artificial RNA bearing low resemblance with any known gene).

You can either normalize the fold change (Case A) or find fold change of the normalized expression (Case B). 

Means the same mathematically.

Case A:

$E_{gene}^{-\Delta Ct_{gene}} / E_{ref}^{-\Delta Ct_{ref}}$

Case B:

$\large\frac{[E_{gene}^{-Ct^{treated}_{gene}}]/[E_{ref}^{-Ct^{treated}_{ref}}]} {[E_{gene}^{-Ct^{control}_{gene}}]/[E_{ref}^{-Ct^{control}_{ref}}]}$

You can rearrange the numerator and denominator to get Case A from Case B. I'm not sure how you are ending up getting different values. Recheck once. It may be because of numerical approximation errors. 

Case A looks much neater; so it is best to calculate that way :)

Real time PCR normalization algorithm
I'm an artist and amateur web designer.

On my portfolio website, I've grouped my work into projects. Most of my projects contain few (20 or less) images, so I just display them in full size and let the visitor scroll (example) because this is how I prefer to browse other artist's work as well.

For projects containing more images, I use thumbnails which link to the full-sized images, because, again, when I browse other artist's portfolios, if there are lots of images on a page it's kinda cumbersome to load. 

Recently I wrote some jQuery to implement a lightbox effect (modal window overlay) so when you click on a thumbnail, the full-sized image appears (example).

My main reasons for implementing this:


it's much more presentable than having a direct link to the image,
which is what I used to do
if the visitor shares the image on something like tumblr or
Pinterest, the link back will be to the project page instead of a
direct link to the image
if the visitor wants to right-click on the thumbnails to load several
images in several new browser tabs/windows, they can still do so (the
lightbox is triggered on left click)


I did not include a close button because it seems like more work for the visitor to have to look for a close button, than to simply click anywhere to close the lightbox (which is what I did).

What are your thoughts regarding lightbox interface for this particular use?
The goal would be the best way to showcase visual art/design work, and the target audience would be, well, anyone who wants to view the work. The display method, in this case a lightbox interface, should be efficient, useable, and presentable (it should highlight, not detract from, the work).
