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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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Error processing batch files #138

Open aishwaryachander opened 3 years ago

aishwaryachander commented 3 years ago

Hi, I was trying to run Immunarch on DNANexus and was unable to process more than 3 files at a time. The tool was unable to create TSNE plots and the process got halted.

This was the code segment:

imm_ov_morisita <- repOverlap(immdata$data, .method = "morisita", .verbose = F) vis(repOverlapAnalysis(imm_ov_morisita, "tsne", .perp=perplexity, .k=n_samples))

This is the produced error message: Warning message: In joined[[col_a]] * joined[[col_b]] : NAs produced by integer overflow Error in na.fail.default(X) : missing values in object Calls: vis ... Rtsne.dist -> as.matrix -> na.fail -> na.fail.default

Unsure what to do next & looking forward to hearing from you!

Regards, Aishwarya Chander

aishwaryachander commented 3 years ago

Hi, Just a quick follow up on this issue as it's a matter of urgency. Ran a few more files and got the same set of errors, and my project is stuck mid-way! Looking forward to hearing from you ASAP. Regards,
Aishwarya Chander

vadimnazarov commented 3 years ago

Hi @aishwaryachander

Thank you for using Immunarch! The package is free and open source software, it's supported by our company and a part of our drug development and analytics platform. We would like to help everyone, but sadly, we are limited in resources. However, we could discuss a commercial-grade support for Immunarch if you think it would be helpful. It includes fast response rates. Please contact me at support@immunomind.io to discuss more details.

Regarding your issue. I wasn't able to reproduce it. How many samples do you have? What is the value of n_samples? What is the value of perplexity? What is the value of imm_ov_morisita?