Clustering issue

Hi, Please note that I am using the following code for clustering, but I got this error “Number of clustered events: 0/119 (0.000000%), Impossible to calculate silhouette score. Only 1 cluster group identified” suppa.py clusterEvents --dpsi cold_cond.dpsi --psivec cold_cond.psivec --sig-threshold 0.05 --eps 0.05 --min-pts 20 --groups 1-4,5-8 -o salt

I don’t know what that means!! Please help, Thanks in advance

Nour

[EduEyras]

Dear Nour,

In the wiki page we give some ideas to visualize results https://github.com/comprna/SUPPA/wiki/SUPPA2-tutorial

In the SUPPA2 paper, we simply plot PSI values along the different time points.

SUPPA2 calculation of events also gives the events in GTF format that you can either use in UCSC or with a different tool for visualisation.

I hope this helps

best

Eduardo

On Mon, 2 Nov 2020 at 01:15, Nourelislam [e-mail] wrote:

Dear Eduardo,

Thank you so much for your response. Did you recommend any tool for visualizing the results of SUPPA2! Actually, I am looking for tool to visualize the local events between conditions!

Thanks for your help,

Nour

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[EduEyras]

Dear Nour,

thanks for your message. This is not really an error. It simply states that only no clusters could be formed using those parameters. Accordingly, the silhouette score cannot be calculated.

Please try changing the parameters for the clustering, like --eps, –min-pts,… to reduce the thresholds to form clusters.

I hope this helps

Best

Eduardo

On Sat, 31 Oct 2020 at 23:20, Nourelislam [e-mail] wrote:

Hi, Please note that I am using the following code for clustering, but I got this error “Number of clustered events: 0/119 (0.000000%), Impossible to calculate silhouette score. Only 1 cluster group identified” suppa.py clusterEvents --dpsi cold_cond.dpsi --psivec cold_cond.psivec –sig-threshold 0.05 --eps 0.05 --min-pts 20 --groups 1-4,5-8 -o salt

I don’t know what that means!! Please help, Thanks in advance

Nour

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/107, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7WHE73RW7MIICY7GLSNP6HLANCNFSM4TF3RVOQ .

– Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ