[adegenet-forum] question on scaleGen()

[Da Pan]

Dear Thimbaut and adegenet users,
Thank you for your time and help.
I probably have some more naif questions about adegenet.
I am attemping a PCA analysis on my SNP dataset with the following
arguements:

test <- read.structure("batch_1.str",n.ind = 17, n.loc =  12451, col.lab =
1, col.pop = 2, row.marknames = 1, NA.char = "0")

test2 <- scaleGen(test, NA.method = "mean")

After this, the R shows:

Warning message:
In .local(x, ...) : Some scaling values are null.
 Corresponding alleles are removed.

I checked pop(test), it returned as :

 1  3  5  7  9 11 13 15 17 19 21 23 25 27 29 31 33
02 02 04 04 06 06 07 07 19 19 38 38 39 39 46 46 46
Levels: 02 04 06 07 19 38 39 46

How to solve this problem?

thanks in advance

Best wishes,
Da
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20161125/8c3c9c6d/attachment-0001.html>