I performed triplicate extractions (technical repeats) from the same batch of plant material. This was done for 40 plant species. Each of the triplicate extracts were analysed via LCMS. I therefore have 40 X 3 = 120 chromatograms.
I used Masslynx 4.1 software.
I now want to perform statistical analysis using MarkerLynx function on MassLynx program. I want to compare the 40 plant species profiles to each other using Principal Component Analysis (PCA). Before I do the statistical analysis to compare the similarities between my 40 plant species, I would like to average the triplicate data of each plant using MarkerLynx? Is this statistically proper? And is it possible to do this using MarkerLynx?
Thanks
Statistically it is valid to average the three triplicates since they are three different extractions. It might be better for t-test or anova test purposes, not so sure that the PCA will benefit greatly from it unless the replicate data is very noisy. Unfortunately I don't know the MarkerLynx software so can't help you there.
Hello Chris
From my point of view, I would have the following considerations:
1. If you use PCA for comparison, it would be nice to build one model also withouth averaging. Since PCA shows you similarities, you would expect to have the 3 points for the same plant as close as possible from one another.
2. The problem, in this case, is not only about averaging the 3 replicates, but also that you have too many groups (40!). Due to that, seeing patterns in PCA can be really difficult and not clear. As Sigurður suggested, I also believe that univariate statistics would be more interesting in your case. You can perform Heat Map Analysis on samples, and also calculate correlation coefficients in order to have a better view of the similarities and differences among the 40 types of plants.
As Sigurður, I do not have experience with MarkerLynx, but these univariate analysis I suggested can be performed online for free in Metaboanalyst
Hope this helps you.
Thank you Vinicius for the suggestions,
From the 40 plants, the largest subset group of plants I will do PCA with will be 30 plants and the smallest will be 2 plants. I will be comparing 15 groups in total, depending on taxonomy, bioactivity etc.
Thanks again
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