NA generated while using all generated Peers while applying cis-eqtl

[Asppagh]

I have generated 30 peers using PEER package on my dataset of 146 samples.
Including all of the peers along with other covariates to run cis-eqtl analysis on my cohorts generated NA in p-values, however if I include only 15 first peers every thing goes well.
Interesting point is if I only include peers #16 -30 everything is ok with it.
Could anyone know what could be the cause pf the issue?

[lp2]

Dear Ahmad, thank you for the report. Ricard (cc-d) has folded PEER into the multi-omics factor analysis (MOFA) framework as described below - we recommend using this going forward, as it is properly supported, and it may resolve your issues. Leo From Ricard: Running MOFA (https://github.com/bioFAM/MOFA2) with one view is effectively PEER. We have also added functionalities and visualisations to interpret the factors before regressing them out for eQTL mapping or any other downstream analysis. I’ve built a wrapper here: https://github.com/bioFAM/PEER Let me know if you have any questions. We have a Slack channel where I provide individualised help. The link is in the MOFA2 github. We have not made the official release yet as we would like to get some feedback how this is working and how intuitive this is. Please let me know about your experience Best, Ricard.

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On Fri, Oct 1, 2021 at 4:18 PM Ahmad.Samiei ***@***.***> wrote: I have generated 30 peers using PEER package on my dataset of 146 samples. Including all of the peers along with other covariates to run cis-eqtl analysis on my cohorts generated NA in p-values, however if I include only 15 first peers every thing goes well. Interesting point is if I only include peers #16 -30 everything is ok with it. Could anyone know what could be the cause pf the issue? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADIQI7E75TF7JCRIPLMQLTUEXGNRANCNFSM5FE5THGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.