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jishnu-lab / SLIDE

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Error: No latent factors are being inputted. #27

Closed Shumin96 closed 5 months ago

Shumin96 commented 5 months ago

I have tried the example data, SLIDE went well. When I used my own bulk-RNA seq data, it initally went well. The input file went through _checkDataParams(input_params)_successfully. However, after a few hours of computing, it reported an error as follows: Output stored in C:/out/0.01_0.5_out/plotInteractions.png No id variables; using all as measure variables Scale for x is already present. Adding another scale for x, which will replace the existing scale. Saving 4.24 x 1.81 in image Error in calcZMatrix(x_std, all_latent_factors, x_path = NULL, lf_path = NULL, : No latent factors are being inputted. error kable checkdata

How can I deal with it?

Hanxi-002 commented 5 months ago

Hi, Thank you for submitting a Github issue.

Your YAML file contains variables "delta1" "delta2" "lambda1" "lambda2". These are unknown parameters to SLIDE, please adjust them into a format as shown in the example YAML file. To summarize, when you read the variable "input_params", which should be a list format in R, "delta" and "lambda" should be an array.

If the problem persists after this, please let us know. Thank you.

Shumin96 commented 5 months ago

Hi, The YAML file contains variables "delta1" "delta2" "lambda1" "lambda2", which is same as the example file in the pdf manual.   After trials, I found it is probably due to the thresh_fdr parameter. When making it bigger, SLIDE went well.

Thanks again for your kind help.

------------------ 原始邮件 ------------------ 发件人: "jishnu-lab/SLIDE" @.>; 发送时间: 2024年4月16日(星期二) 晚上8:02 @.>; @.**@.>; 主题: Re: [jishnu-lab/SLIDE] Error: No latent factors are being inputted. (Issue #27)

Hi, Thank you for submitting a Github issue.

Your YAML file contains variables "delta1" "delta2" "lambda1" "lambda2". These are unknown parameters to SLIDE, please adjust them into a format as shown in the example YAML file. To summarize, when you read the variable "input_params", which should be a list format in R, "delta" and "lambda" should be an array.

If the problem persists after this, please let us know. Thank you.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Hanxi-002 commented 5 months ago

So glad you were able to run SLIDE successfully!