The mass spectra of five different samples were generated. How can I perform PCA using the m/z obtained for these samples to identify the variation between them? I am not familiar with PCA at all so I need ideas and tutorials that can help me.
Hi Chukwuemeka,
Can you give more information about your data and let me know if you have access to Xlstat software?
Hi,
in order to carry out a principal compenent analysis you should arrange your data in a matrix (I x J) with as much rows (I) as your samples and columns (J) as variables. I have never worked with m/z data in such a way but I suppose that you should set as variables your m/z values. In this way you will have for each sample the relative mass spectrum. Then, once performed the PCA, you will be able to see how them (the variables) are span in the space of PCs and how your samples (scores) will be distributed in this space also.
For example, in IR spectroscopy, the matrix is composed of samples (rows) and wavenumbers (columns) which, all together, represent the sample spectrum.
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