Hello, I have 2 scRNA-Seq data set for 2 conditions. There is not any batch effect. Tissues, platforms, date of experiments are completely identical. Only difference is condition so if I do a batch correction, I would lose the information I need so I analyzed each data set seperately. I processed, clustered and identified cell types.
Now I want to to trajectory analysis of a specific cell type in both of the condition. To do that, I used subset function to create cell type specific Seurat object and merged them. After that, should I use counts data and start the analysis with Monocle 3 from the beginning or should I create CDS object with normalized data and directly order cells?
Thank you in advance.
@ Friederike @ hkarakurt , Hi guys, I am a beginner in slingshot, I also want to use seurat object to run the slingshot, but I ran these issues: 1. how to right load the seurat object? I used the as.SingleCellExperiment, but it displayed <object with="" null="" pointer="">, which will affect my analysis. Is there any other way I can run integrated seurat object in slingshot?
Many thinks,
Yale Liu
Please create a new question for this since it is not related to original question in this thread not is it an answer to the original question.
I agree with Genomax: please post this as a separate question, I'll try to assist there. Please also use the proper formatting for code portions (e.g. make use of the button with 101010) so that it's easier to understand what you did.