Jess

plotIndiv() does not retain group colours from factor levels

1

plotIndiv refuses to keep the factor levels I want... this is because it is a numeric so orders values like 100 before values like 11. How do I use the...

Hi, this is not an issue but more a question relating to single cell data analysis in Seurat. I think it is just a more general question about integration so...

Error with vars.to.regress: "contrasts can be applied only to factors with 2 or more levels"

6

When running: `soup_obj levels(soup_obj$Sex) [1] "Male" "Female" ``` Seurat_5.0.3 EDIT: I also get this when I try to use many levels: ``` Regressing out batch Error in `contrasts levels(soup_obj$batch) [1]...

IntegrateLayers using FastMNN gives error: 'batch' must be specified if '...' has only one object

2

I'm trying to run FastMNN on a Seurat object from an existing analysis where I previously used Harmony integration but now I want the expression values to be batch corrected...

Error running on cellbender adjusted counts

5

Hi, I've run cellbender on my data and read the filtered count matrix into R using `Read_CellBender_h5_Mat` from scCustomize and then converted that to a Seurat object using `CreateSeuratObject`. I'm...

Warning to PrepSCTFindMarkers when I already have

7

Hi, trying to run `FindAllMarkers` on SCT transformed data: ``` # find markers for each cluster seu

I'm trying to SCTransform each sample separately but then find variable features across all samples. The samples are basically identical so do not need "integration". This is my LogNormalisation pipeline...

make_sampleqc_report can not find "setorder"

1

Hi - I'm trying to follow the tutorial and getting the following error: ``` > make_sampleqc_report(qc_obj, save_dir, proj_name) rendering Quitting from lines 118-124 [plot_beta_k] (SampleQC_report_template.Rmd) Something went wrong with rendering...

Error reading h5seurat file

2

``` h5ad_file