[adegenet-forum] Large scale on PCA axes

[Linda Rutledge]

Hi,

I have produced several PCAs on a large SNP dataset using the "genlight" object and the glPca function. The new package is working great.

My concern is that in the PCAs I've produced, the scale on the PC1 (~13%) and PC2 (~3%) axes are very large (-30 to +30 on PC1 and -10 to +40 on PC2). This seems rather strange to me since most of my searching suggests typical axes ranges to be tenfold less and a similar analysis in a different program with differing groups has ranges -0.2 to 0.4. It does seems that most of the variation is explained in the first PC but this doesn't seem to change drastically with different groupings of the data.

Is it possible that the large range of the PCA suggests there is a problem in the dataset? or perhaps the analyses?

Thanks.

Linda