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 ***@***.***> 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 <#2 (comment)>, 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 ***@***.***> 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 ***@***.*** ***@***.***>> 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 <#2 (comment)>, 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 ***@***.***> 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 ***@***.***> 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 ***@***.*** ***@***.***>> 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 <#2 (comment)>, 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 <#2 (comment)>, 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 ***@***.***> 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 ***@***.***> 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 ***@***.*** ***@***.***>> 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 <#2 (comment)>, 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 <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AntUsbSBM9D_jT5m1V0e7uwbvrtg37UVks5uJzGrgaJpZM4VAy4S>.

[juanbot]

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

km2gcn is not maintained anymore.