[R] Aligning gel data

john seers (IFR)
Fri, 26 Oct 2007 14:45:42 -0000

Hello R

I have some data from a number of gels showing the distance of bands in
each gel and lane. My problem is to align these values by some method.

It has been suggested to me (by a Matlab expert) that I could use
Spectral methods such as COW (correlation-optimised warping) or PAGA
(peak alignment using GA). I have searched but cannot find if there are
equivalent packages that do this in R. Any suggestions from anybody on
where to look? The idea is, I think, to create a matrix of all the
possible values, mark them as present or not, and then perform an
alignment.

i.e a matrix something like:

		lane1 lane2 lane3 ...
	.001	1	0	0	etc
	.002	0	0	0	etc
	.003
	...

Is there a more direct method than using spectral methods? Has anybody
done something equivalent?

Thank you in advance for any help.


Regards


John Seers