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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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X and Y variables : Reliability test #60

Open AlexisFon opened 8 months ago

AlexisFon commented 8 months ago

Hi,

I have two questions :

  1. How can we use single cell data normalized with SCT ? I have the following error : Error in as.matrix(sc_dataset@assays$RNA@data) : no slot of name "data" for this object of class "Assay5" and if i replace in the code _scdataset@assays$RNA@data, by _scdataset@assays$SCT@data, I have 0 cells identified, no matter the alpha value.

  2. I perform SCISSOR analysis on my data (with classic RNA assay) and want to do the reliability test. However, I don't know what I have to put instead X and Y variables in the function : result2 <- reliability.test(X, Y, network, alpha = 0.05, family = "binomial", cell_num = numbers, n = 50, nfold = 10).

Does someone have the answer to these questions ?

sudawq commented 6 months ago

Q1.Maybe you can try "scedata[["RNA"]] <- as(scedata[["RNA"]], "Assay")"

Namuhan33 commented 5 months ago

Q2 if you load the workspace that's been save from scissor function, X and Y are within it