Hi,
When I try to run the « plotExpression » function of « scater » R package as described in this tutorial https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette-dataviz.html , an error occurs:
> plotExpression(example_sce, rownames(example_sce)[1:6], x = "Mutation_Status", exprs_values = "counts")
Error in .subset2(x, i, exact = exact) : no such index at level 1
Errors is triggered only when x corresponds to a “colData” of my “SingleCellExperiment” object and not when x corresponds to a “rowname” of the same object:
> plotExpression(example_sce, rownames(example_sce)[1:6], x = "Gene_0002", exprs_values = "logcounts")
No Error
[version of Bioconductor packages: “scater” = 1.6.3 & “SingleCellExperiment” = 1.0.0]
Please help
Thanks!
Could you try using the latest version of SingleCellExperiment (1.2.*) and scater (1.8.*)?
In my case Rstudio points to R 3.4 version. And upgrading R may impact a lot.
Both SingleCellExperiment (1.2.*) and scater (1.8.*) requires R (>= 3.5).
Look. Let's assume there is a bug in the old version of scater. Even if I were to fix the bug, I would only push the bugfix to the latest version of scater. So you'd have to download and install the latest version anyway.
As a developer, I can only guarantee the performance of the current versions of all packages. If you use old versions, I can't help much with bugs; and nor do I want to, because I probably fixed them in the latest version.
It is possible to have multiple versions of R installed, and to tell RStudio to use one or another, so that you can install a current R and current Bioconductor without disrupting your R 3.4 installation. Some hints may be found at https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#managing-multiple-versions and by googling RSTUDIO_WHICH_R
Hello Martin,
Thanks for reply!
It worked in different environment with SingleCellExperiment (1.2.0) and scater (1.8.2).
I had some production data where I am using R 3.4. and having user base 100+ .It may impact to other user if i will update RSTUDIO_WHICH_R.
Is there any other way.
Thanks!