Harmony converged after 6 iterations Error in UseMethod(generic = "Key", object = object) : no applicable method for 'Key'...

ncedi12 commented 9 months ago

hi there I'm encountering this issue when trying to run harmony integration on seurat platform

Harmony converged after 6 iterations Error in UseMethod(generic = "Key", object = object) : no applicable method for 'Key' applied to an object of class "character"

this was the command: after SCT and RunPCA.

object <- RunHarmony(object, group.by.vars =c('orig.ident','Subgroup'), assay.use = "SCT", theta = c(0.5,2))

or

object <- RunHarmony(object, group.by.vars =c('orig.ident','Subgroup'), assay.use = "SCT", reduction = 'pca', theta = c(0.5,2))

All give the same error as above..

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: AlmaLinux 8.8 (Sapphire Caracal)

Matrix products: default BLAS: /hpf/tools/R/4.0.3/lib64/R/lib/libRblas.so LAPACK: /hpf/tools/R/4.0.3/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=C LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] magrittr_2.0.3 glue_1.6.2 sctransform_0.3.2 harmony_0.1.1
[5] Rcpp_1.0.10 SeuratObject_4.0.0 Seurat_4.0.0

I've tried passing a single group.by.vars argument, or single theta (doesn't allow this with two group.by argument.

any advice on how to deal with this error?

pati-ni commented 9 months ago

I can see you are using Harmony v0.1.1. Can you please upgrade the harmony package and retry?

sallyseullee-0821 commented 8 months ago

Hi @pati-ni, I am facing a similar issue, but my harmony package is version 1.2.0. When I run the following,

integrated<- RunHarmony(seurat, group.by.vars = c("samples"), reduction.save = T, plot_convergence = TRUE)

I receive an error:

Harmony converged after 6 iterations
Error in UseMethod(generic = "Key", object = object) : 
  no applicable method for 'Key' applied to an object of class "logical"

I would appreciate your guidance on solving this issue. Thank you!

pati-ni commented 8 months ago

What is the Seurat version you are using?

On Sun, Jan 14, 2024, 23:12 sallyseullee-0821 @.***> wrote:

Hi @pati-ni https://github.com/pati-ni, I am facing a similar issue, but my harmony package is version 1.2.0. When I run the following,

integrated<- RunHarmony(seurat, group.by.vars = c("samples"), reduction.save = T, plot_convergence = TRUE)

I receive an error:

Harmony converged after 6 iterations Error in UseMethod(generic = "Key", object = object) : no applicable method for 'Key' applied to an object of class "logical"

I would appreciate your guidance on solving this issue. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/immunogenomics/harmony/issues/221#issuecomment-1891273298, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSFW2EFYOQNGFFB5MZFUDLYOSUBNAVCNFSM6AAAAAA7R6CE26VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJRGI3TGMRZHA . You are receiving this because you were mentioned.Message ID: @.***>

ShuqingL commented 3 days ago

hello @pati-ni, I encountered the same problem. R version 3.6.1, harmony package is version 1.2.0 Previously, there was no problem using it, but this time there is a problem and I don't know how to solve it. The current usage is single-cell transcriptome data, with two samples.

immunogenomics / harmony