[adegenet-forum] Error

[Jombart, Thibaut]

Hello, 

apparently you end up with not a single global principal component, which is fairly odd. I would think there is a problem in your dataset. Can you check that you can actually perform a basic PCA on the genetic data? It may also be good looking for missing locations.

Cheers

Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Sandhya Sekar [sandysek at gmail.com]
Sent: 18 August 2011 11:56
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Error

Dear adegenet users,
I have been trying sPCA on two datasets that I have. These are binary datasets generated with AFLP. While things went smooth as ice with the first, the second is giving me the following error:

# start of error
spca1 <- spca (dat1, cn = CN, scannf = F)
Error in names(auxi) <- paste("CS", agarder, sep = "") :
  'names' attribute [3] must be the same length as the vector [2]
In addition: Warning message:
In multispati(dudi = pcaX, listw = resCN, scannf = scannf, nfposi = nfposi,  :
  There are only 0 positive factors.

# end of error

The CN works fine, gets plotted well. The same thing works well on my other dataset. I have tried many things, but nothing seems to work! I would like some help on this one.

Sandhya



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Sandhya Sekar
PhD student
Center for Ecological Sciences
Indian Institute of Science
sandhya at ces.iisc.ernet.in<mailto:sandhya at ces.iisc.ernet.in>