[adegenet-forum] Missing data in sPCA

[michael fontaine]

Dear all,

The function na.replace seems to have disappear from the last version of ADEGENET 2.0.1.

Now, one can use scaleGen()  or tab() to replace missing data by the “mean”, for example. However the returned object is a frequency table. It seems that the spca() function does not accept frequencies since adegenet 2.0.0.  What is the recommended procedure to replace missing data by the mean and conduct a sPCA? 

Furthermore, I am using the jitter function to put some noise around my coordinates. It worked very well in the former version. In this new version, the sPCA tells me that it has found duplicates. I have checked the coordinates with noise, and there are none. Not sure what’s going on.

Is there any similar report from other user?

I am looking forward you advices.

Thanks in advance 

Michael
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