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huBioinfo / CytoTalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.
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Error in compNodePrize_Combine(OutputPath) : can not find object 'TypA_ind' #2

Closed JimmyLuo-WJ closed 3 years ago

JimmyLuo-WJ commented 3 years ago

Dear developer, Cytotalk version 3.0.1 is really friendly to use and I have tried it to analyze my scRNA-seq data. But I got an error and have no idea how to deal with the problem. Could you help me with? Thank you very much.

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huBioinfo commented 3 years ago

Dear Jimmy, Thanks for your usage of CytoTalk 3.0.1 and reporting your issues. For your case, I think it's probably because your specified input parameter "CellTypeA" is not consistent to the naming of your input files "scRNAseqxxx.csv". For example, if your "CellTypeA" is defined as "Fibroblasts", your input scRNA-seq data file should be named as "scRNAseqFibroblasts.csv". In this way, the intermediate parameter "TypA_ind" should then have a value. The consistent naming for "CellTypeB" should be also guaranteed. Please let me know if this problem can be addressed using this way. Thanks!

JimmyLuo-WJ commented 3 years ago

Dear developer, My problem can truly be addressed by using this way! Thank you very much. I do input the file with wrong name which is no consistent to the parameter "CellTypeA". I just checked it and the error did not happen again. But when generating the final signaling network at step 6, another error occurs: "Subscript out of bounds" (or Subscript out of range). I have no idea what's going on.

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huBioinfo commented 3 years ago

Dear Jimmy, Can you give me a screenshot for the generated files (sorted by modified time) in the /Output/ folder, which could give me a clue for this issue. Thanks!

JimmyLuo-WJ commented 3 years ago

Dear developer, No problem. Here are generated files in my output folder.

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huBioinfo commented 3 years ago

Hi Jimmy, Sorry for the late reply. Do you have 100 subfolders (with prefix "bt") under your /Output/ folder? If so, I'm also confused with this problem. If it's convenient for you, can you share the /Output/ folder with me via some tools and I'll look into this problem. The /Output/ folder does not include any raw data, just intermediate results. Looking forward to your reply. Thanks!

JimmyLuo-WJ commented 3 years ago

Dear developer,

This problem also confused me. I uploaded my output files to the google drive and the link is as below. Please check it. Thanks.

https://drive.google.com/drive/folders/1-XmPXP3Qv-CwyMI3kYwqfTvbx7Vhjftg?usp=sharing

羅偉嘉 Wei-Jia Luo Ph.D student Tel: +886-2-2312-3456 ext 66923

Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University. Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist., Taipei City 100, Taiwan (R.O.C.).

寄件者: huBioinfo @.> 回覆: huBioinfo/CytoTalk @.> 日期: 2021年5月17日 星期一 下午5:46 收件者: huBioinfo/CytoTalk @.> 副本: JimmyLuo-WJ @.>, Author @.***> 主旨: Re: [huBioinfo/CytoTalk] Error in compNodePrize_Combine(OutputPath) : can not find object 'TypA_ind' (#2)

Hi Jimmy, Sorry for the late reply. Do you have 100 subfolders (with prefix "bt") under your /Output/ folder? If so, I'm also confused with this problem. If it's convenient for you, can you share the /Output/ folder with me via some tools and I'll look into this problem. The /Output/ folder does not include any raw data, just intermediate results. Looking forward to your reply. Thanks!

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JimmyLuo-WJ commented 3 years ago

Dear developer, Sure. I just upload my output files to google drives and send the link to your mail address. Please check it.

huBioinfo commented 3 years ago

Dear Jimmy, I'm downloading it. Will try to give you feedback soon. Thanks!

huBioinfo commented 3 years ago

Dear Jimmy,

I've found the problem and fixed it by revising the script "deter_W4.R" under the /Input/ folder in the latest package "CytoTalk_package_v3.0.2". Please download it from https://github.com/huBioinfo/CytoTalk/releases/tag/v3.0.2 Thank you so much for making an important contribution to improving this package!!! Hope everything goes well with the latest one.

JimmyLuo-WJ commented 3 years ago

Dear developer,

I have downloaded the latest version of Cytotalk (v3.0.2) and my data went well with it. The output folder /IllustratePCSF/ was successfully generated. Thank you very much for helping me.