Threshold and phenotypic variation values expectation from PRSice are wrong in the tutorial

[flaviaerius]

I have noticed after following the full tutorial of PLINK and PRSice that both have the same expectation values in the questions below the following links:

• PLINK
• PRSice

From my results, the threshold for PLINK is indeed 0.3, as said in the answers, but for PRSice it is actually 0.13995 by following the tutorial.
Same for the phenotypic variation, which for PLINK is indeed 0.1612372, but for PRSice the PRS.R2 is 0.162601.

I see this has already been addressed on this issue, but I decided to create a new issue to address this specific problem, since the other issue is less specific.

I know this is old now, but this came up when I was working with a student learning about PRS. She was worried that her results did not match with the tutorial. I believe other people have the same problem and might think there is something wrong with their results, that is why I decided to open the issue!

Thank you for the great work overall!

[choishingwan]

Hi, thanks for the information. Unfortunately, I don't really have time since I left academic. I will keep this in mind and try to fix that when I have time. Sam

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On Thu, Jul 25, 2024 at 10:29 AM Flávia Eichemberger Rius < ***@***.***> wrote: I have noticed after following the full tutorial of PLINK and PRSice that both have the same expectation values in the questions below the following links: - PLINK <https://choishingwan.github.io/PRS-Tutorial/plink/#finding-the-best-fit-prs> - PRSice <https://choishingwan.github.io/PRS-Tutorial/prsice/#running-prs-analysis> From my results, the threshold for PLINK is indeed 0.3, as said in the answers, but for PRSice it is actually 0.13995 by following the tutorial. Same for the phenotypic variation, which for PLINK is indeed 0.1612372, but for PRSice the PRS.R2 is 0.162601. I see this has already been addressed on this issue <#22 (comment)>, but I decided to create a new issue to address this specific problem, since the other issue is less specific. I know this is old now, but this came up when I was working with a student learning about PRS. She was worried that her results did not match with the tutorial. I believe other people have the same problem and might think there is something wrong with their results, that is why I decided to open the issue! Thank you for the great work overall! — Reply to this email directly, view it on GitHub <#55>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYV3Z5T3VMBJZL5OX53ZOEDS3AVCNFSM6AAAAABLOVZ5CKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQZTAMJSGAYTSNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>