[adegenet-forum] question about warning message

Jombart, Thibaut t.jombart at imperial.ac.uk
Wed Sep 23 16:03:07 CEST 2015

Dear Ella,

this is hard to tell without the input file. However, you may want to use genind objects for that kind of data, as the dataset is fairly small. genlight only is recommended when basically no other options are available, i.e. 100,000 or millions of SNPs


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Ella Bowles [ebowles at ucalgary.ca]
Sent: 22 September 2015 20:28
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] question about warning message


After I converted my data into a genlight object, I got the warning message
Warning message:
In matrix(txt, ncol = 4, byrow = TRUE) :
  data length [16397] is not a sub-multiple or multiple of the number of rows [4100]

How do I know if this is a problem?

I have just over 4000 SNPs spread over 186 individuals. My data import line is:

data=read.PLINK(file='plink.raw', map.file='batch_1.plink.map', quiet = FALSE, chunkSize = 186, parallel = FALSE)

With thanks,

Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: ebowles at ucalgary.ca<mailto:ebowles at ucalgary.ca>, bowlese at gmail.com<mailto:bowlese at gmail.com>
website: http://ellabowlesphd.wordpress.com/
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