Optimizing the interactions in the network produced an error

[saezlab]

Optimizing the interactions in the network produced an error

[deeenes]

Hi @adesalegn,

Your top level call here is mlrmbo_optimization, which is a function from nichenetr. Have you tried to ask them? https://github.com/saeyslab/nichenetr/issues The error is deep in the nichenet code, which I have little knowledge about, in OmnipathR we only have a thin wrapper around it.

In general, I would check if the igraph, mlrMBO, mlr, parallelMap and nichenetr packages are all the latest versions. If you've run your code successfully before, I would check for recent updates, e.g. new igraph came out 2 months ago. Would be also interesting if you experience the error with any input or only for certain networks? I think in NicheNet errors are often related to particular network topologies, especially disconnected components.

Best,

Denes

[adesalegn]

Hi deeenes, Thank you for the reply. However, is there any possibility to download the following files Results/Optimization_results.rds, Results/weighted_networksNonSourceWeights.rds, Results/ligand_target_matrixNoweights.rds, Results/ligand_target_matrixWithweights.rds, Results/weighted_networksWithSourceWeights.rds Thank you! Best, AD

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On Wed, Dec 22, 2021 at 12:03 PM deeenes ***@***.***> wrote: Hi @adesalegn <https://github.com/adesalegn>, Your top level call here is mlrmbo_optimization, which is a function from nichenetr. Have you tried to ask them? https://github.com/saeyslab/nichenetr/issues The error is deep in the nichenet code, which I have little knowledge about, in OmnipathR we only have a thin wrapper around it. In general, I would check if the igraph, mlrMBO, mlr, parallelMap and nichenetr packages are all the latest versions. If you've run your code successfully before, I would check for recent updates, e.g. new igraph came out 2 months ago. Would be also interesting if you experience the error with any input or only for certain networks? I think in NicheNet errors are often related to particular network topologies, especially disconnected components. Best, Denes — Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANYNSRF56KIT2HSOJTYJZ5TUSGWA3ANCNFSM5KRNDSIA> . 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>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[deeenes]

Hi,

Is this about the case study in last years paper? This is the repository of the case study, where you can find the necessary information, or ask Alberto.

Best,

Denes

[alberto-valdeolivas]

Hello @adesalegn,

Sorry, I missed this message. In case you are still interested in these files, could you send me your email? I can deposit them in some location and share them with you. Some of the files are too big for github.

Best,
Alberto.

[adesalegn]

Sure, here it is. ***@***.*** Thanks!

…

On Mon, May 2, 2022, 10:24 Alberto Valdeolivas ***@***.***> wrote: Hello @adesalegn <https://github.com/adesalegn>, Sorry, I missed this message. In case you are still interested in these files, could you send me your email? I can deposit them in some location and share them with you. Some of the files are too big for github. Best, Alberto. — Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANYNSRCKYXHEZBNP2NFSWZ3VH6GLNANCNFSM5KRNDSIA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[alberto-valdeolivas]

Hello,

I generated a shareable link containing the files. Let me know if it works

https://1drv.ms/u/s!AsEej4TsWiVfgeAnQyVo40qn0Tcn8g?e=p94Ofb

Alberto