immunomind
Error processing batch files
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
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
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 [email protected] 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?
