different qmatrix each time I run?

[Dahn-YoungDong]

LanGen_pipeline_version2/1.1_FILTERING_SNPs.R

Lines 847 to 849 in d98a65e

	set.seed(13)
	for (i in lambda_values){
	tess3.ls = tess3(genotypes, coord = coordinates, K = K, mask = mask, lambda = i,

Hello Jeronymo, Thanks for your help along the way.

Whenever I rerun the tess3 function, I receive a different qmatrix, and result in different ancestry proportions for my barplot. Why is it so? Should I do the "set.seed()?"

I adapted your code and took out the loop and lambda parameter.

`K = c(1:5) # set the number of K to be tested
ploidy = 2 # species ploidy
CPU = 4 #Number of cores for run in parallel

tess3.ls <- tess3(X = genotypes, coord = coordinates, K = K,
method = "projected.ls", ploidy = ploidy, openMP.core.num = CPU)

q.matrix <- qmatrix(tess3.ls, K = 5)

my.colors <- c(1:5)
my.palette <- CreatePalette(my.colors, 6)
barplot(q.matrix, border = T, space = 0,
main = "Ancestry matrix",
xlab = "Individuals", ylab = "Ancestry proportions",
col.palette = my.palette) -> bp
axis(1, at = 0.5:nrow(q.matrix), labels = snps@meta[,3][bp$order], las = 3, cex.axis = 1)
`

[Dahn-YoungDong]

Is it possible to access your Pilocarpus dataset so that I can run your tutorial code as it was originally written for?

Best,

[jdalapicolla]

Thanks for the updated code. Unfortunately, this dataset is not published so I can't send to you one copy. I'm sorry. Best, *Jeronymo Dalapicolla* Biólogo | Biologist | CRBio 91.859/02-D Instituto Tecnológico Vale | Vale Institute of Technology Desenvolvimento Sustentável | Sustainable Development Rua Boaventura da Silva, 955 - Nazaré, Belém, Pará Phone: +55 (19) 998559340 Skype: @jeronymod CV Lattes <http://lattes.cnpq.br/0831988373556961> GitHub <https://github.com/jdalapicolla> Google Scholar <https://scholar.google.com.br/citations?user=09ArXn4AAAAJ&hl=en> ORCID <https://orcid.org/0000-0002-4819-9720> ResearchGate <https://www.researchgate.net/profile/Jeronymo_Dalapicolla> Publons <http://www.researcherid.com/rid/D-4711-2016> AcademiaEdu <https://independent.academia.edu/JeronymoDalapicolla> LinkedIn <https://www.linkedin.com/in/jeronymo-dalapicolla-3862b16b> Em qua., 9 de dez. de 2020 às 18:09, Dahn-Young Dong < [email protected]> escreveu:

…

Is it possible to access your Pilocarpus dataset so that I can run your tutorial code as it was originally written for? Best, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIGPCMFKW52L2DOXJEAJNILST7RQDANCNFSM4UTWYCLA> .