Quang Nguyen

Advice on how to sub-cluster?

8

Hi there, Thanks for the tool! From #161, `run.flowsom` seemed to be unable to break up the big orange cluster but the UMAP seemed to suggest there are potentially more...

Exported channel values do not agree with what was shown in FlowJo Biex?

7

Hi there, Thanks again for the tool and your help so far! I hope to get clarification on why the exported channel values do not agree with the numerical values...

transpose = T/F in make.pheatmap() produced inconsistent results

3

Hi there, Thank you for the package. When I plotted the same data and markers but with `transpose=T` or `transpose = F`, the expression for markers per cluster were different....

Is skipping data transformation for channel values in Spectre workflow only is specific to the Spectre workflow?

2

Hi there, Thanks for the package. [1] According to issue #121, `Spectre::read.files()` is a wrapper around `flowCore::read.flowSet` or `flowCore::read.FCS`. [2] From the discussion here (https://github.com/RGLab/flowCore/issues/245), `flowCore` read functions apply a...

Real or technical artifacts due to errors detected in UMAP following run.flowsom()?

2

Hi there, Thanks for the package. When I used `run.flowsom` even with `meta.k=20` (automatic `meta.k` resolved 11 clusters), the cluster UMAP doesn't look "right" -- they clumped together on 1...

Adjust pc.range in IKAP for SCTransform()-processed Seurat objects?

6

Dear @NHLBI-BCB and @xizhihui Thank you for developing the package! I have processed my data using SCTransform() (which replaces NormalizeData(), ScaleData() and FindVariableFeatures()) and have performed RunPCA, RunUMAP, FindNeighbors() and...

Why does the highest expression plotted with most negative density? Disagreement between FeaturePlot vs plot_density

7

Hi there, Thanks for a great tool. I plot the joint density of a vector of genes that were scored using AddModuleScore. When I plotted this score for each cell...

Hi all, Thank you so much again for your patience and continued support. I look forward to new updates. In the mean time, I wonder if you could help me...

Hi there, Thank you very much for the tool. I was hoping to get clarification regarding the order in which one should run `iDEA.BMA()` and the variant iDEA.fit model. After...

`WhichCell()` for marker names with dashes from `ADT` assay returned error of `None of the requested variables were found`, even when using backticks

1

Hi there, I have a Seurat object with both RNA and ADT assay data. Anyone has any input why `WhichCells()` failed to retrieve the cells using ADT markers? ``` DefaultAssay(gem_ID.list_MERGED)...