Matrix

[LaptopY]

Hello, In order to apply CellRouter to my own datasets in the future, I would like to try to complete (and master) your tutorial with the mouse bone marrow single-cell RNA-sequencing dataset (I am a new user in R). You mentionned at the beginning of the tutorial that "CellRouter assumes that you are providing a gene expression matrix with genes as rows and single-cells as columns." I understand that these are the normalized and filtered_expression files provided.

However, I was wondering how to obtain in the future the file named "matrix.R" that you use in "Create Cell Router" part. It is a matrix with two columns and single cells in rownames. You mentioned to rename these columns as tSNE1 and tSNE2, so I assumed that this matrix could come from a "tsne analysis", is it correct or am I wrong ?

I tried to do this with filtered_expression files using fdata1<-t(fdata) # transposition "test<-Rtsne(as.matrix(fdata1), dims=2, check_duplicates=FALSE, pca=T, perplexity=30, theta=0.5, max_iter = 5000) matrix <- as.data.frame(test$Y) # matrix 2 columns 1007 rows Using this matrix I obtained a different graph, "similar" but different.

could you indicate me what are the main steps to obtain this "matrix" ? (I apologize for my English)

Thank you