Cannot extract p-values from cluster comparisons

[sg3451]

Is there a way to extract the p-values from the 'testClusters' function? The output is currently a list with 2 elements but none of them contain statistical significance results. One element of the list appears to be a dendogram but it is hard to interpret it.

[igrabski]

Hi, the p-values are printed after the colon next to the node/cluster labels in the dendrogram-type output (the second element of the list). They can be interpreted as the p-value corresponding to splitting that node/cluster. If no p-value is printed next to any particular cluster, it's because no further split was evaluated within that cluster (e.g. no further split may be possible if that cluster already represents one of the original inputted clusters).

[sg3451]

Thanks very much for the prompt response! Just so I understand it correctly, in the following output, the splits at Node 0, Node 1, Node 2 and Node 3 are significant. Ultimately, scSHC is reporting 5 clusters based on the node splits (named Cluster 1-5) - is this correct? There are no further splits from any of these 5 clusters? Node 0: 0 2 ¦--Node 1: 0 3 ¦ ¦--Cluster 1 4 ¦ °--Node 3: 0 5 ¦ ¦--Cluster 4 6 ¦ °--Cluster 5 7 °--Node 2: 0 8 ¦--Cluster 2 9 °--Cluster 3

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On Wed, May 29, 2024 at 4:03 PM igrabski ***@***.***> wrote: Hi, the p-values are printed after the colon next to the node/cluster labels in the dendrogram-type output (the second element of the list). They can be interpreted as the p-value corresponding to splitting that node/cluster. If no p-value is printed next to any particular cluster, it's because no further split was evaluated within that cluster (e.g. no further split may be possible if that cluster already represents one of the original inputted clusters). — Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AR4XNDP5BDPFLMU3KUETNF3ZEY7CLAVCNFSM6AAAAABIPVQVDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZYGI3DAMRXGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[igrabski]

Yes that is correct!

[sg3451]

Excellent - thank you again for the quick response. I appreciate it. Regards, Sujoy

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On Thu, May 30, 2024 at 10:14 AM igrabski ***@***.***> wrote: Yes that is correct! — Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AR4XNDNAUBSWBEQBTLPPYPLZE465HAVCNFSM6AAAAABIPVQVDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZZHA4DOMJWGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>