Can't load sce data

[JihedC]

Hi,
I am new to Ouija but quite excite about using it.
I have got my Seurat object transformed into a singleCellExperiment object. Unfortunately Ouija doesn't seem to see like this. I get this :

oui <- ouija(sample1.sce)
Error in t.default(x@assays[[single_cell_experiment_assay]]) : 
  argument is not a matrix

Am I doing something wrong?

[kieranrcampbell]

Hi Jihed Did you get this working? I’m currently trying to debug but there are issues using Stan on MacOS Catalina that I’m looking into

…

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[JihedC]

Hi Kieran!
Thanks for your reply!
No I didn't manage to load the singlecellexperiment I created via Seurat. I tried to work around it by importing a matrix from my Seurat object.

expression <- as.matrix(sample@assays$RNA@data)
test <- expression[1:10,1:100]
transposed<-t(test)
test <- transposed +1
normalized_test <- log(test)

oui <- ouija(test)
plot_expression(oui)

But I have no clue if this is okay to do so. I have got this plot:

[kieranrcampbell]

Hmm looks like the sampler hasn't run at all. Let me debug over the next few days and see where I get. I suspect various dependencies have been updated that have broken the main package.

[JihedC]

ok thanks!
I have also tried to run your example with Singlecellexperiment:

library(ouija)
data(synth_gex)
single_cell_set <- SingleCellExperiment(assays = list(exprs = t(example_gex)))
ouija(single_cell_set)

Which also gives the same output :

Error in t.default(x@assays[[single_cell_experiment_assay]]) : 
  argument is not a matrix

[kieranrcampbell]

Ok that error should now be fixed in c77e652 -- can you reinstall from github and try again? Thanks

[JihedC]

Yep I'll have a look

[JihedC]

Ok that error should now be fixed in c77e652 -- can you reinstall from github and try again? Thanks

Nope I still get the same error message and the command :

data(synth_gex)

doesn't work anymore :(

[kieranrcampbell]

Okay at some point synth_gex became example_gex -- can you try that? I've updated doc in latest commit

[JihedC]

This is what I've got. Sorry it's in French, it means that the argument is not a matrix :(

> data(example_gex)
> single_cell_set <- SingleCellExperiment(assays = list(exprs = t(example_gex)))
> ouija(single_cell_set)
Error in t.default(x@assays[[single_cell_experiment_assay]]) : 
  l'argument n'est pas une matrice
> 

[kieranrcampbell]

Ah the assay should be "logcounts" or the single_cell_experiment_assay changed to "logcounts" -- I've updated the vignette to reflect this, my fault for not changing sooner. Also it looks like you haven't reinstalled from github since I just changed the code to remove the line x@assays... -- could you reinstall using devtools::install_github and try again? Thanks

[JihedC]

I reinstalled earlier using this

devtools::install_github("kieranrcampbell/ouija")

I'll try again

[JihedC]

Ah the assay should be "logcounts" or the single_cell_experiment_assay changed to "logcounts" -- I've updated the vignette to reflect this, my fault for not changing sooner. Also it looks like you haven't reinstalled from github since I just changed the code to remove the line x@assays... -- could you reinstall using devtools::install_github and try again? Thanks

I am afraid I am not understanding what you mean. Which command should I use to load the ice assay?

By the way these are my session info (concerning the installation):

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS  10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /anaconda3/envs/seurat/lib/R/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ouija_0.99.0                sctransform_0.2.0           rstan_2.19.2                ggplot2_3.2.1              
 [5] StanHeaders_2.19.0          Rcpp_1.0.3                  Seurat_3.1.1                knitr_1.26                 
 [9] SingleCellExperiment_1.4.1  SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6        
[13] matrixStats_0.55.0          Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.2        
[17] IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0   

[kieranrcampbell]

single_cell_set <- SingleCellExperiment(assays = list(logcounts = t(example_gex)))
ouija(single_cell_set)

should work ?

I've also bumped the version number so if you get the same error as before (Error in t.default(x@assays[[single_cell_experiment_assay]]) ) can you reinstall and ensure version number is
0.99.1 ? Thanks