Hi all, I need to do some quality control on a two channel Agilent dataset, of which unfortunately I can't retrieve the raw data. The values are in log ratios and when I do a PCA I can't see any meaningful clustering but rather all the points are clumped together. Are the log ratios causing that or it just shows there isn't much going on biologically? if the problem are the log ratios is there a sensible way to transform them or carry out other kind of PCAs? Thanks a lot
So you are doing PCA on a matrix of probes and logFC, where each logFC column comes from a two-colour array. I'm not sure in this case PCA can give anything meaningful since it depends on what samples have been paired, unless one channel is always a reference common to all the arrays.
It might be possible to extract the individual intensities if you have the intensity value of each spot besides the logFC value.