Issue when running km2gcn

[milddaa]

Hello,

I am trying to implement your package km2gcn on own set of data to refine modules and it seems to run well at first but then I get the following error:

[1] "Starting partition 1" [1] "Number of centroids before getting new partition 38" Error in cor(x, y, use, method = "pearson", quick, nThreads, verbose, : When 'weights.x' are given, they must be a vector of length 'nrow(x)' or a matrix of the same dimensions as 'x'.

I am still an amateur programmer so I do not understand where this error is coming from. Do you perhaps know?

Thank you in advance!

[crewrob]

Hi any luck with this? I'm having the same issue and a hard time debugging. Thanks!

[juanbot]

Sorry about that, can you go to the source

and change

WGCNA::corFast

with simply

cor

every time it appears?

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:16, crewrob notifications@github.com wrote:

Hi any luck with this? I'm having the same issue and a hard time debugging. Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407422505, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWLNEMf-6-5zhkOgITJs2zflpcQHRKLks5uJyxFgaJpZM4VAy4S.

[juanbot]

Hi again, in the meantime, please also check

https://github.com/juanbot/coexp/ https://github.com/juanbot/coexp/

It is the improved version

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:38, Juan A. Botía juanbotiablaya@gmail.com wrote:

Sorry about that, can you go to the source

and change

WGCNA::corFast

with simply

cor

every time it appears?

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:16, crewrob <notifications@github.com mailto:notifications@github.com> wrote:

Hi any luck with this? I'm having the same issue and a hard time debugging. Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407422505, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWLNEMf-6-5zhkOgITJs2zflpcQHRKLks5uJyxFgaJpZM4VAy4S.

[crewrob]

ok am looking at the new package which will take some time. I’m fairly new to R, do you have source package with the edits? Am having hard time figuring out how to edit the source of the installed package. Many many thanks!

On Jul 24, 2018, at 10:39 AM, Juan A. Botía notifications@github.com wrote:

Hi again, in the meantime, please also check

https://github.com/juanbot/coexp/ https://github.com/juanbot/coexp/

It is the improved version

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:38, Juan A. Botía juanbotiablaya@gmail.com wrote:

Sorry about that, can you go to the source

and change

WGCNA::corFast

with simply

cor

every time it appears?

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:16, crewrob <notifications@github.com mailto:notifications@github.com> wrote:

Hi any luck with this? I'm having the same issue and a hard time debugging. Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407422505, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWLNEMf-6-5zhkOgITJs2zflpcQHRKLks5uJyxFgaJpZM4VAy4S.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407430850, or mute the thread https://github.com/notifications/unsubscribe-auth/AntUsbSBM9D_jT5m1V0e7uwbvrtg37UVks5uJzGrgaJpZM4VAy4S.

[crewrob]

Hi Juan,

Persistence pays off, I wrote:

trace("corDistance",edit=TRUE) # Change two instances of WGCNA::corFast to cor

And made the edit on the fly, even though I’ll have to do this at runtime. Of course I’ll be using your new package soon anyways.

Thanks again!

• Robert

On Jul 24, 2018, at 10:39 AM, Juan A. Botía notifications@github.com wrote:

Hi again, in the meantime, please also check

https://github.com/juanbot/coexp/ https://github.com/juanbot/coexp/

It is the improved version

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:38, Juan A. Botía juanbotiablaya@gmail.com wrote:

Sorry about that, can you go to the source

and change

WGCNA::corFast

with simply

cor

every time it appears?

---

Juan A. Botía Reader in Computer Science and Artificial Intelligence, Universidad de Murcia, Spain Hon. Senior Research Fellow, Institute of Neurology, University College London, UK

On 24 Jul 2018, at 16:16, crewrob <notifications@github.com mailto:notifications@github.com> wrote:

Hi any luck with this? I'm having the same issue and a hard time debugging. Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407422505, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWLNEMf-6-5zhkOgITJs2zflpcQHRKLks5uJyxFgaJpZM4VAy4S.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/juanbot/km2gcn/issues/2#issuecomment-407430850, or mute the thread https://github.com/notifications/unsubscribe-auth/AntUsbSBM9D_jT5m1V0e7uwbvrtg37UVks5uJzGrgaJpZM4VAy4S.

[juanbot]

Check http://github.com/juanbot/CoExpNets.

km2gcn is not maintained anymore.