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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Error in tutorial trajectory analysis #2225

Open alekseybelikov opened 2 hours ago

alekseybelikov commented 2 hours ago

Attach your log file ArchR-correlateTrajectories-32567050e2a2-Date-2024-10-25_Time-19-19-59.909418.log

Describe the bug trajCombined <- trajGSM2 assay(trajCombined) <- t(apply(assay(trajGSM2), 1, scale)) + t(apply(assay(trajMM2), 1, scale))

Error in assays<-(*tmp*, withDimnames = withDimnames, ..., value = *vtmp*): please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x, withDimnames=FALSE)) <- value' when the rownames or colnames of the supplied assay(s) are not identical to those of the receiving SummarizedExperiment object 'x'

To Reproduce Reproducible in the tutorial

Expected behavior Step completed without error

rcorces commented 2 hours ago

Hi @alekseybelikov! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

alekseybelikov commented 2 hours ago

okay, this is actually solved in https://github.com/GreenleafLab/ArchR/discussions/1375#discussioncomment-2510919 perhaps the code in the tutorial should be updated too