Open zhongguozhiwang opened 1 year ago
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@zhongguozhiwang Did you solve the problem?
Hi,
Try experimenting with the different hclust_methods:
-
'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best.
On Fri, Jul 5, 2024 at 8:24 AM sjasws @.***> wrote:
@zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem?
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Here's the list of options: ("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid")
On Sat, Jul 6, 2024 at 8:19 AM Brian Haas @.***> wrote:
Hi,
Try experimenting with the different hclust_methods:
-
'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best.
On Fri, Jul 5, 2024 at 8:24 AM sjasws @.***> wrote:
@zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem?
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>
--
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclust_method='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error.
I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem?
I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation.
On Sat, Jul 6, 2024 at 8:32 AM sjasws @.***> wrote:
Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error.
I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem?
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211756983, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.***>
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation. … On Sat, Jul 6, 2024 at 8:32 AM sjasws @.> wrote: Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 (comment) <#591 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error. I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem? — Reply to this email directly, view it on GitHub <#591 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
In that case, I'll have to use infercnv's auto-generated figures. In any case, thank you very much to your team for providing such an excellent tool, which has helped me to infer tumor cells and their subclones.
Great! I'm hoping we'll be back on track with supporting it again in the not too distant future.
On Sat, Jul 6, 2024 at 8:51 AM sjasws @.***> wrote:
I don't think so. We don't have anyone working on the project at the moment, and I haven't touched the codebase in years now - plus don't have time to support it, unfortunately. Tis the situation. … <#m7995038566241453533> On Sat, Jul 6, 2024 at 8:32 AM sjasws @.*> wrote: Hi, Try experimenting with the different hclust_methods: - 'infercnv::run(hclustmethod='ward.D2') : the clustering method to use. All built-in R hclust methods are supported. We find 'ward.D2' (default) to work best. … <#m-5484367672227859767_> On Fri, Jul 5, 2024 at 8:24 AM sjasws @.> wrote: @zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang https://github.com/zhongguozhiwang Did you solve the problem? — Reply to this email directly, view it on GitHub <#591 https://github.com/broadinstitute/infercnv/issues/591 (comment) <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2210785101>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE https://github.com/notifications/unsubscribe-auth/ABZRKXZH7WE34PSTKVLWZWLZK2GAVAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQG44DKMJQGE . You are receiving this because you are subscribed to this thread.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas http://broad.mit.edu/~bhaas Thank you, I just used the default Settings and have passed all the procedures. But when I go back to draw my own heatmap with plot_cnv function, I always get this error: Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error. I also found that many people suffer from the same problem, but it doesn't seem to be solved. Have you solved the problem? — Reply to this email directly, view it on GitHub <#591 (comment) https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211756983>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM https://github.com/notifications/unsubscribe-auth/ABZRKX3KJOVP2NXYTT7ASZTZK7PUTAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG42TMOJYGM . You are receiving this because you commented.Message ID: @.***> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
In that case, I'll have to use infercnv's auto-generated figures. In any case, thank you very much to your team for providing such an excellent tool, which has helped me to infer tumor cells and their subclones.
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/infercnv/issues/591#issuecomment-2211761255, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX74BAPCQLLPGJQUWETZK7R6RAVCNFSM6AAAAABKNDPSKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJRG43DCMRVGU . You are receiving this because you commented.Message ID: @.***>
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
INFO [2023-08-25 20:19:52] ::plot_cnv:Start INFO [2023-08-25 20:19:52] ::plot_cnv:Current data dimensions (r,c)=9400,8897 Total=83707578.1686258 Min=0.805765388786346 Max=4.9614932171772. INFO [2023-08-25 20:19:53] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2023-08-25 20:19:54] plot_cnv(): auto thresholding at: (0.900934 , 1.100879) INFO [2023-08-25 20:19:55] plot_cnv_observation:Start INFO [2023-08-25 20:19:55] Observation data size: Cells= 8513 Genes= 9400 ERROR [2023-08-25 20:19:55] Unexpected error, should not happen. Error in .plot_cnv_observations(infercnv_obj = infercnv_obj, obs_data = obs_data, : Error