I am analyzing genetic variation among 26 individuals of Physalis angulata using RAPD method. I got 16 locus as the result. I have to analyze the result using PCA in SPSS. I've searched in many source but every source gave different step and no one of them have example of similar case of RAPD. i've try several time but still dont get the result of plot showing the grouping of individuals.
This shouldn't be too difficult. Why don't you try other programs such as Ntsys and/or Genalex, they are very user-friendly and since your data set is small, the PC analysis will be very consistent regardless of the stats you apply. I would also advise to test your data with other multivariate options, in particular similarity values and phonetic associations. That info can also give you insights on how critical is conducting a PCA.
You can perform PCA using OriginLab software. It's very easy and user friendly software. Give a read to following link.
http://www.originlab.com/doc/Tutorials/Principal-Component-Analysis
Hope it helps.
I am a factor analyst `(and know more than somewhat about SPSS) but not a geneticist so I am not clear about your data but from you description you have data on 16 locus for 26 individuals, which could be a 16 (rows) by 26 (columns) matrix - or flipping it over (a 26 row by 16 col table). SPSS will only do principal components on the columns. The number of components you can find for the 26 individuals is a maximum of 16 (the max rank of the matrix). If this is your data it is very easy to enter it into spss (which also reads text or excel files) and the pull-down menus Analyze > Dimension Reduction > Factor gives you a menu where your can include your variables and indicate (in the Extraction box) that you wish to do Principal Components.(the default). Click OK and you are there.
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