2DE image analysis
tonnomartinez
I am Toño Martínez, and I join the group incorporating a need in order
to get help. I hope this kind of questions could also foster the
group.
As I exposed in the Jornadas in Córdoba, we need to analyze 2DE gels
in a way the commercial packages do not do, as we label PTMs with
different colours, in a DIGE-like fashion, but without being a DIGE.
I have looked at digeR package recently published, but it does
statistical analysis after the image analysis. We would need to modify
the workflows of the image analysis
Do you have any clue of the following?
- any solution already described
- people who could help or who wantedd to get involved in developing a
solution for this.
Thank you,
Toño
Alex_PCB
I haven't used 2D gels for long time so I can't really help you with
details. However, I recall a couple things that could help you out.
1) an freely available (I believe you could get the code upon request)
software for 2D analysis from Jeff Morris named PINNACLE
you can find the software for downloading on this page (look for a
link on the right side all way to the bottom of the web page)
http://works.bepress.com/jeffrey_s_morris/35/
2) A couple years ago, I played with a software named SCISOFT. This
thing sounds a little crazy. This is a software used in Astronomy for
"counting" stars in the sky and determine patterns. I heard about
someone who was implementing this software to analyze protein spots
("the stars") in 2D gels ("the sky"). The advantage is that it is
completely open, and quite robust. The disadvantage is that it is
quite complicated.
3) R bioconductor provides a number of package to analyze DNA
microarrays. In a sense, the setup is quite similar to 2D gels with
fluorescence. Obviously, you would need to change the code of these
programs. Again, they are all open-source.
good luck!!!!
alex