<div dir="ltr">Dear Maike, <div><br></div><div>no, the ordering of alleles should not change anything. See for instance using sim2pop:</div><div><br></div><div><div>> library(adegenet)</div><div><br></div><div>> data(sim2pop)</div><div> /// adegenet 2.0.1 is loaded ////////////</div><div><br></div><div> > overview: '?adegenet'</div><div> > tutorials/doc/questions: 'adegenetWeb()' </div><div> > bug reports/feature requests: adegenetIssues()</div><div><br></div><div><br></div><div>> dapc1 <- dapc(tab(sim2pop), grp=pop(sim2pop), n.pca=10, n.da=1)</div><div><br></div><div>> dapc2 <- dapc(tab(sim2pop)[,sample(1:ncol(tab(sim2pop)))], grp=pop(sim2pop), n.pca=10, n.da=1)</div><div><br></div><div>> dapc1$eig</div><div>[1] 484.1916</div><div><br></div><div>> dapc2$eig</div><div>[1] 484.1916</div><div><br></div><div>> dapc1$li</div><div><br></div><div>> sum(dapc1$ind.coord-dapc2$ind.coord)</div><div>[1] -1.110223e-16 # this is a zero</div><div><br></div></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology<br></div></div>Imperial College London<br><a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><br></div><div><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br></a></div>Twitter: <a href="https://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 27 June 2016 at 13:40, <span dir="ltr"><<a href="mailto:herrmann-m@uni-landau.de" target="_blank">herrmann-m@uni-landau.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div style="FONT-SIZE:12pt;FONT-FAMILY:'Calibri';COLOR:#000000">
<div>Hi!</div>
<div> </div>
<div>I was performing pairwise DAPCs on a data set containing > 62.000 SNPs
in 4 populations. </div>
<div> </div>
<div>Because of a problem with my PLINK input, my SNPs were initially in a
“wrong” order. When I noticed the error, I repeated the DAPC analysis with a
correctly ordered input file, primarily to get correct SNP-IDs for the allele
loadings. Thereby I noticed differences between the two analyses:</div>
<div>Individual coordinates (dapc$ind.scores) and DAPC eigenvalues (dapc$eig)
differed and allele loadings (dapc$var.contr) were also slightly different. The
output of find.clusters was not different between the input files.</div>
<div> </div>
<div>My code:</div>
<div>> data1 <- read.PLINK("file.raw", map.file = NULL, quiet = FALSE,
chunkSize = 1000, parallel = FALSE)</div>
<div>> clust1 <- find.clusters(data1, stat="BIC", choose.n.clust=TRUE,
max.n.clust=10, n.iter=1e5, n.start=10, pca.select="percVar",
perc.pca=100, glPca=NULL, parallel=FALSE)</div>
<div>> dapc1 <- dapc(data1, pop = clust1$grp, pca.select = "percVar",
perc.pca = 100, parallel=FALSE)</div>
<div>> loadings1 <- dapc1$var.contr</div>
<div>> ld1 <- loadings1[order(loadings1[,1], decreasing = TRUE),]</div>
<div>> write.table(ld1, file = "PW1_loadings_rc.txt")</div>
<div> </div>
<div>DAPC Output 1 (unsorted SNPs): </div>
<div>$eig (eigenvalues): 8.495e+32 vector length
content
</div>
<div>$ind.scores</div>
<div> LD1</div>
<div>Cluster1 -8.413869e+15 #(same value for
all 6 individuals in this cluster)</div>
<div>Cluster2 8.413869e+15 #(same value for
all 6 individuals in this cluster)</div>
<div>$var.contr (in decreasing order)</div>
<div>[line 72] "60732" 0.000171552889525985</div>
<div>[line 72] "2993" 0.000154678359525634</div>
<div>[line 72] "976" 0.000152483049214648</div>
<div> </div>
<div>DAPC Output 2 (correctly sorted SNPs):</div>
<div>$eig (eigenvalues): 4.459e+33 vector length
content </div>
<div>$ind.scores</div>
<div> LD1</div>
<div>Cluster1 -1.927727e+16 #(same value for
all 6 individuals in this cluster)</div>
<div>Cluster2 1.927727e+16 #(same value for
all 6 individuals in this cluster)</div>
<div>$var.contr (in decreasing order) </div>
<div>[line 72] "60819" 0.000171552889525985</div>
<div>[line 73] "42995" 0.000154678359525636</div>
<div>[line 74] "697" 0.000152483049214647</div>
<div>(-> of course the SNP-IDs don’t match, but the values in each line of
the output should correspond )</div>
<div> </div>
<div>I used exactly the same code and the only difference between the analyses
was the sorting of SNPs. I realize that the difference in allele loadings (my
main interest) is marginal but I was surprised to find differences in the first
place. Is that normal? Shouldn’t these results be independent from the sorting
of SNPs? Could it be because of rounding errors? </div>
<div> </div>
<div> </div>
<div>Thank you for your time!</div>
<div>Cheers,</div>
<div>Maike</div>
<div> </div>
<div> </div>
<div> </div>
<div> </div>
<div> </div>
<div> </div>
<div> </div></div></div></div>
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