Re: Normalization without all bead channels?
mleipold wrote:Hi Santhosh,
Unfortunately, none of the current methods (Fluidigm, MATLAB/Premessa) will work without all the five major EQ bead channels. And there's no way to "recover" data that was never collected in the first place (since it wasn't in your template).
The best chance you would have would be to talk to someone who could modify the normalization script(s) to leave out the missing channel.
Mike
An alternative could be the CATALYST package: https://catalyst-project.github.io/.
There is an implementation of the Finck normalization where you specify the channels you want to use.
There are also at least 3 entry points: 1. The R package itself, if you write your own scripts; 2. Local web interface,
where you install all the packages locally to your R installation and run a web-based app from R; 3. The web-based app http://imlspenticton.uzh.ch:3838/CATALYSTLite/ (can be slow, has some file size limits, more for exploring than production use).
Best, Mark