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