Dear all,
My question deals with the command which performs Principal Component Analysis (PCA). I use an input matrix of pairwise distances
calculated from percentage residue identity of a multiple protein sequence alignment.
I executed the following script :
#################
env = environ()
aln = alignment(env, file='alignment.pir')
aln.id_table(matrix_file='id.mat')
env.principal_components(matrix_file='id.mat', file='alignment_mod..princ')
#################
The file 'alignment_mod.princ' contains projected coordinates of the first two principal components..
I compared these results with other programs which hold PCA and go by the same input matrix.
For instance, ade4, a package of the R software.
I executed the following commands under R :
#################
require (ade4)
x <- read.table("id.mat", sep="")
y <- dudi.pca(x, scan = F, nf = 2)
write.table(y$li, file = "alignment_ade4.princ")
#################
The file 'alignment_ade4.princ' also contains projected coordinates of the first two principal components.
However, the coordinates acquired with these two softwares are not the same.
I would like to know if the PCA command of Modeller uses internal procedures which could explain this disagreement ? How does the treatment of input matrix work with Modeller ?
Any help on this will be greatly appreciated.
Best regards, Julien