[adegenet-forum] Missing data in sPCA

[Thibaut Jombart]

Dear Michael,

good point. I'll fix this tomorrow. I have posted an issue from your post:

https://github.com/thibautjombart/adegenet/issues/143

Follow it to track progress.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 3 June 2016 at 15:44, michael fontaine <mikafontaine at gmail.com> wrote:

> 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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