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cran / OptM

:exclamation: This is a read-only mirror of the CRAN R package repository. OptM — Estimating the Optimal Number of Migration Edges from 'Treemix'
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SD is zero for 1 or more runs! Check your analysis #2

Open linhai1221 opened 1 year ago

linhai1221 commented 1 year ago

how to solve the problem "SD is zero for 1 or more runs! Check your analysis"

gaborcsardi commented 1 year ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Look for Maintainer, BugReports and URL. Thanks!

teyiatia commented 1 year ago

Hi, linhai1221. I encountered the same problem when running this software. How did you finally solve it?

linhai1221 commented 1 year ago

no，i use treemix heatmap to judge.

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---- Replied Message ---- | From | @.> | | Date | 01/31/2023 17:40 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [cran/OptM] SD is zero for 1 or more runs! Check your analysis (Issue #2) |

Hi, linhai1221. I encountered the same problem when running this software. How did you finally solve it?

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teyiatia commented 1 year ago

thank you so much. I just retrieved an article. they prevented bootstrapped TreeMix runs from having an SD = 0 by down sampling the LD-corrected VCF file to 80% of total SNP sites, randomly drawn over 10 replicates using the bcftools -view command. Article links: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001890 I do not know if it works, I will try tonight, how do you think?

9879879871 commented 1 month ago

@teyiatia Hello, have you resolved the issue