Teadora Tyler

4 Questions 3 Answers 0 Followers

Questions related from Teadora Tyler

(scRNAseq) Is it recommended to filter out cells with high % of mitochondrial genes in tumor tissue?

Mitochondria evidently have important roles in cancer development and progression. So when preprocessing single cell data generated from tumor tissue, is it wise to apply the "standard" filtering...

21 August 2023 4,507 2 View

What kind of correction is recommended today in 2D manual cell counting (in brain tissue) for estimating cell density?

What is the current opinion about the Abercrombie-correction and its modifications? Most literature I find on the topic is at least 20 years old.

07 March 2022 1,309 1 View

How do I interpret an interaction between variables in a linear mixed model?

For example, I have a 2-level factor variable (diagnose) in interaction with a 6-level factor variable (layer). Intercept by default is the first level of all. In my case intercept is control...

19 September 2020 6,371 4 View

Why do scRNAseq pipelines (e.g. seurat) have the filtering step to remove cells that express over 2500 genes? Meaning, why 2500?

Does anyone know how this number became "default"? what is it based on? How deep is our knowledge of "average" , "healthy" gene expression of different cell types? Sorry if my question is trivial...

05 August 2020 6,950 1 View