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JSB-UCLA / scDesign2

An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated
MIT License
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When I run my own dataset, I get the following Error. What might be the cause? #7

Open DongShengze opened 1 week ago

DongShengze commented 1 week ago

This dataset works on both splatter and zinb-wave, but it didn't work when I followed the tutorial simulation of a single type of cell:

copula_result <- fit_model_scDesign2(data_mat, 'type', sim_method = 'copula') Error in pnbinom(gene, size = param[2], mu = param[3]) : 数学函数中用了非数值参数 此外: There were 50 or more warnings (use warnings() to see the first 50) warnings() 警告信息： 1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 2: In sqrt(1/i) : 产生了NaNs 3: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 4: In sqrt(1/i) : 产生了NaNs 5: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 6: In sqrt(1/i) : 产生了NaNs 7: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 8: In sqrt(1/i) : 产生了NaNs 9: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 10: In sqrt(1/i) : 产生了NaNs 11: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 12: In sqrt(1/i) : 产生了NaNs 13: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 14: In sqrt(1/i) : 产生了NaNs 15: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 16: In sqrt(1/i) : 产生了NaNs 17: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 18: In sqrt(1/i) : 产生了NaNs 19: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 20: In sqrt(1/i) : 产生了NaNs 21: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 22: In sqrt(1/i) : 产生了NaNs 23: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 24: In sqrt(1/i) : 产生了NaNs 25: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 26: In sqrt(1/i) : 产生了NaNs 27: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 28: In sqrt(1/i) : 产生了NaNs 29: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 30: In sqrt(1/i) : 产生了NaNs 31: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 32: In sqrt(1/i) : 产生了NaNs 33: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 34: In sqrt(1/i) : 产生了NaNs 35: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 36: In sqrt(1/i) : 产生了NaNs 37: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 38: In sqrt(1/i) : 产生了NaNs 39: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 40: In sqrt(1/i) : 产生了NaNs 41: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 42: In sqrt(1/i) : 产生了NaNs 43: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 44: In sqrt(1/i) : 产生了NaNs 45: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 46: In sqrt(1/i) : 产生了NaNs 47: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 48: In sqrt(1/i) : 产生了NaNs 49: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 50: In sqrt(1/i) : 产生了NaNs

If you can provide some tips or help, I would really appreciate it!

JSB-UCLA commented 1 week ago

Please provide your input dataset or its exact format, and I hope my student Qingyang can help address the issue you encountered or suggest whether scDesign3 can help.

Best, Jessica

On Wed, Oct 23, 2024 at 8:43 PM Ca @.***> wrote:

This dataset works on both splatter and zinb-wave, but it didn't work when I followed the tutorial simulation of a single type of cell:

copula_result <- fit_model_scDesign2(data_mat, 'type', sim_method = 'copula') Error in pnbinom(gene, size = param[2], mu = param[3]) : 数学函数中用了非数值参数 此外: There were 50 or more warnings (use warnings() to see the first 50) warnings() 警告信息： 1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 2: In sqrt(1/i) : 产生了NaNs 3: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 4: In sqrt(1/i) : 产生了NaNs 5: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 6: In sqrt(1/i) : 产生了NaNs 7: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 8: In sqrt(1/i) : 产生了NaNs 9: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 10: In sqrt(1/i) : 产生了NaNs 11: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 12: In sqrt(1/i) : 产生了NaNs 13: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 14: In sqrt(1/i) : 产生了NaNs 15: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 16: In sqrt(1/i) : 产生了NaNs 17: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 18: In sqrt(1/i) : 产生了NaNs 19: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 20: In sqrt(1/i) : 产生了NaNs 21: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 22: In sqrt(1/i) : 产生了NaNs 23: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 24: In sqrt(1/i) : 产生了NaNs 25: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 26: In sqrt(1/i) : 产生了NaNs 27: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 28: In sqrt(1/i) : 产生了NaNs 29: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 30: In sqrt(1/i) : 产生了NaNs 31: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 32: In sqrt(1/i) : 产生了NaNs 33: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 34: In sqrt(1/i) : 产生了NaNs 35: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 36: In sqrt(1/i) : 产生了NaNs 37: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 38: In sqrt(1/i) : 产生了NaNs 39: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 40: In sqrt(1/i) : 产生了NaNs 41: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 42: In sqrt(1/i) : 产生了NaNs 43: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 44: In sqrt(1/i) : 产生了NaNs 45: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 46: In sqrt(1/i) : 产生了NaNs 47: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 48: In sqrt(1/i) : 产生了NaNs 49: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 50: In sqrt(1/i) : 产生了NaNs

If you can provide some tips or help, I would really appreciate it!

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DongShengze commented 6 days ago

Thanks a lot for your reply!

Please check the dataset that attached to this email. What I'm providing is a float array, and when I use it, I'm rounding it to integer. This is a gene subset of the original dataset, containing 2000 hypervariable genes with a total of 1422 samples. All samples share the same cell-type. I want to generate an equal number of samples with scDesign2. My error may have been due to my lack of experience with R, but I didn't know what to do. I would appreciate it if you could give me some help.

At 2024-10-23 22:22:02, "Junction of Statistics and Biology" @.***> wrote:

Please provide your input dataset or its exact format, and I hope my student Qingyang can help address the issue you encountered or suggest whether scDesign3 can help.

Best, Jessica

On Wed, Oct 23, 2024 at 8:43 PM Ca @.***> wrote:

This dataset works on both splatter and zinb-wave, but it didn't work when I followed the tutorial simulation of a single type of cell:

copula_result <- fit_model_scDesign2(data_mat, 'type', sim_method = 'copula') Error in pnbinom(gene, size = param[2], mu = param[3]) : 数学函数中用了非数值参数 此外: There were 50 or more warnings (use warnings() to see the first 50) warnings() 警告信息： 1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 2: In sqrt(1/i) : 产生了NaNs 3: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 4: In sqrt(1/i) : 产生了NaNs 5: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 6: In sqrt(1/i) : 产生了NaNs 7: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 8: In sqrt(1/i) : 产生了NaNs 9: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 10: In sqrt(1/i) : 产生了NaNs 11: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 12: In sqrt(1/i) : 产生了NaNs 13: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 14: In sqrt(1/i) : 产生了NaNs 15: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 16: In sqrt(1/i) : 产生了NaNs 17: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 18: In sqrt(1/i) : 产生了NaNs 19: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 20: In sqrt(1/i) : 产生了NaNs 21: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 22: In sqrt(1/i) : 产生了NaNs 23: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 24: In sqrt(1/i) : 产生了NaNs 25: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 26: In sqrt(1/i) : 产生了NaNs 27: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 28: In sqrt(1/i) : 产生了NaNs 29: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 30: In sqrt(1/i) : 产生了NaNs 31: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 32: In sqrt(1/i) : 产生了NaNs 33: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 34: In sqrt(1/i) : 产生了NaNs 35: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 36: In sqrt(1/i) : 产生了NaNs 37: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 38: In sqrt(1/i) : 产生了NaNs 39: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 40: In sqrt(1/i) : 产生了NaNs 41: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 42: In sqrt(1/i) : 产生了NaNs 43: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 44: In sqrt(1/i) : 产生了NaNs 45: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 46: In sqrt(1/i) : 产生了NaNs 47: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 48: In sqrt(1/i) : 产生了NaNs 49: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 50: In sqrt(1/i) : 产生了NaNs

If you can provide some tips or help, I would really appreciate it!

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JSB-UCLA commented 6 days ago

Please directly send an email to me @.) and Qingyang Wang ( @.) with your example dataset and R code. I couldn't see your attachment in the comment. Thanks!

Best, Jessica

On Thu, Oct 24, 2024 at 10:26 AM Ca @.***> wrote:

Thanks a lot for your reply!

Please check the dataset that attached to this email. What I'm providing is a float array, and when I use it, I'm rounding it to integer. This is a gene subset of the original dataset, containing 2000 hypervariable genes with a total of 1422 samples. All samples share the same cell-type. I want to generate an equal number of samples with scDesign2. My error may have been due to my lack of experience with R, but I didn't know what to do. I would appreciate it if you could give me some help.

At 2024-10-23 22:22:02, "Junction of Statistics and Biology" @.***> wrote:

Please provide your input dataset or its exact format, and I hope my student Qingyang can help address the issue you encountered or suggest whether scDesign3 can help.

Best, Jessica

On Wed, Oct 23, 2024 at 8:43 PM Ca @.***> wrote:

This dataset works on both splatter and zinb-wave, but it didn't work when I followed the tutorial simulation of a single type of cell:

copula_result <- fit_model_scDesign2(data_mat, 'type', sim_method = 'copula') Error in pnbinom(gene, size = param[2], mu = param[3]) : 数学函数中用了非数值参数 此外: There were 50 or more warnings (use warnings() to see the first 50) warnings() 警告信息： 1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 2: In sqrt(1/i) : 产生了NaNs 3: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 4: In sqrt(1/i) : 产生了NaNs 5: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 6: In sqrt(1/i) : 产生了NaNs 7: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 8: In sqrt(1/i) : 产生了NaNs 9: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 10: In sqrt(1/i) : 产生了NaNs 11: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 12: In sqrt(1/i) : 产生了NaNs 13: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 14: In sqrt(1/i) : 产生了NaNs 15: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 16: In sqrt(1/i) : 产生了NaNs 17: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 18: In sqrt(1/i) : 产生了NaNs 19: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 20: In sqrt(1/i) : 产生了NaNs 21: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 22: In sqrt(1/i) : 产生了NaNs 23: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 24: In sqrt(1/i) : 产生了NaNs 25: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 26: In sqrt(1/i) : 产生了NaNs 27: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 28: In sqrt(1/i) : 产生了NaNs 29: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 30: In sqrt(1/i) : 产生了NaNs 31: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 32: In sqrt(1/i) : 产生了NaNs 33: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 34: In sqrt(1/i) : 产生了NaNs 35: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 36: In sqrt(1/i) : 产生了NaNs 37: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 38: In sqrt(1/i) : 产生了NaNs 39: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 40: In sqrt(1/i) : 产生了NaNs 41: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 42: In sqrt(1/i) : 产生了NaNs 43: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 44: In sqrt(1/i) : 产生了NaNs 45: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 46: In sqrt(1/i) : 产生了NaNs 47: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 48: In sqrt(1/i) : 产生了NaNs 49: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > ... : iteration limit reached 50: In sqrt(1/i) : 产生了NaNs

If you can provide some tips or help, I would really appreciate it!

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DongShengze commented 6 days ago

I'm sorry but I could not see the email address, they were masked by the website. I have uploaded the file in this comment, maybe you can check that this time. Thank you for your patience. fibroblast_float.zip scDesign2_test_code.zip