Just looking some input on this, as an outsider's opinion is always appreciated!
I'm looking for novel auto-antibodies in patients with disease versus healthy controls. The experiment setup is as follows:
I am extracting protein from a human cell line (specific to the disease) and running 2D PAGE and then transferring the gel by Western blot. The Western blot is then probed with the patients plasma to see if anything binds. I have 30 patients in my disease group and 30 in my control group.
So, in theory I will be running 60 gels/western blots.
The problem arises when I come to compare them. How would I even go about this? I would need to compare within each group and then compare bewteen groups. I have Progenesis software.
Any input would be great including any issues that are obvious?