Function to normalize spectral counts

% Feed in either 1 or 2  ato output normOverlord.  If
% input is 1, the output is the OverlordMatrix
% normalized by columns (down every row), i.e. comparisons can be made
% for relative abundances of proteins in a given sample, e.g. we can
% "compare" protein cadherin-1 to protein IL-2 within sample Peptide A.
If
% the input is 2, the output is the OverlordMatrix
% normalized by rows (across every column), i.e. comparisons can be made
% for the relative abundance of a given protein across all samples, e.g.
we
% can "compare" protein cadherin-1's relative abundance across all
samples
% (Peptides A to ZZ).  Also required is the MOUSE.fasta downloaded from
% UniProt!  Link:
%
http://www.uniprot.org/uniprot/?query=taxonomy%3a10090&sort=score&format=*
% hit download
% UPDATE: If you have MusProt.mat in the working directory, the FASTA
data
% is not needed and the program runs fastA.