Error in { : task 14 failed - "invalid 'length' argument" about methylresolver

[darneson]

Hi Ahwan, I completely understand, however, it is a bit difficult on my end to debug the issue without a reproducible example. The workaround that you propose will work as intended (each sample is considered independently for the deconvolution). The results should be exactly the same if you pass multiple subsets of your ample versus all samples at the same time. Best, Doug

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On Tue, Aug 17, 2021 at 2:36 PM ahwanpandey ***@***.***> wrote: Hi Doug, Thanks for your reply. This is unpublished data so I am a bit hesitant to do that just yet. Since different subsets work, should I just run with a batch of 20 or 30 at a time? Would the end result be the same/similar if I ran all 126 together? Thanks, Ahwan — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC4HWGF754FIJQVUQ2HJUPTT5LIZVANCNFSM5CI6LDFQ> . 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&utm_campaign=notification-email> .

[ahwanpandey]

Different subsets/combinations of the data works but not when I put the whole dataset.

> res = MethylResolver(methylMix = beta_vals[,50:80,drop=FALSE], betaPrime = FALSE, doPar = TRUE, numCores = 6, absolute = TRUE)
Beginning LTS Deconvolution For This Mixture...
  |=====================================================================================================================================| 100%
Error in { : task 4 failed - "invalid 'length' argument"
In addition: There were 12 warnings (use warnings() to see them)

> res = MethylResolver(methylMix = beta_vals[,60:80,drop=FALSE], betaPrime = FALSE, doPar = TRUE, numCores = 6, absolute = TRUE)
Beginning LTS Deconvolution For This Mixture...
  |=====================================================================================================================================| 100%
Completed LTS Deconvolution For This Mixture...

[darneson]

Hello, Is it possible to share your beta_vals matrix with me? It is a bit difficult to debug without seeing the data. Can you post a reproducible example? Best, Doug

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On Mon, Aug 16, 2021 at 8:47 PM ahwanpandey ***@***.***> wrote: Different subsets/combinations of the data works but not when I put the whole dataset. > res = MethylResolver(methylMix = beta_vals[,50:80,drop=FALSE], betaPrime = FALSE, doPar = TRUE, numCores = 6, absolute = TRUE) Beginning LTS Deconvolution For This Mixture... |=====================================================================================================================================| 100% Error in { : task 4 failed - "invalid 'length' argument" In addition: There were 12 warnings (use warnings() to see them) > res = MethylResolver(methylMix = beta_vals[,60:80,drop=FALSE], betaPrime = FALSE, doPar = TRUE, numCores = 6, absolute = TRUE) Beginning LTS Deconvolution For This Mixture... |=====================================================================================================================================| 100% Completed LTS Deconvolution For This Mixture... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC4HWGBNYCQW3QCZJP7WE7DT5HLT5ANCNFSM5CI6LDFQ> . 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&utm_campaign=notification-email> .

[ahwanpandey]

Hi Doug,

Thanks for your reply. This is unpublished data so I am a bit hesitant to do that just yet.

Since different subsets work, should I just run with a batch of 20 or 30 at a time? Would the end result be the same/similar if I ran all 126 together?

Thanks,
Ahwan

[ahwanpandey]

Great thanks for that.