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XZouProjects / scCODE

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data
MIT License
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how to filter the results #6

Open Mengshu123 opened 1 year ago

Mengshu123 commented 1 year ago

Dear XZouProjects Thank you for providing so great DE analysis software, I have severl problems about it. The first one: I would like to understand how to filter the DE_results. Should I exclude genes that were detected less than 5 times? my DE_result is :

table(All_Markers[[1]]$DE_result$Detected_times)

1 2 3 4 4 469 1552 682

The Second one : All_Markers[[i]]=scCODE(data1,data2,light = TRUE,top_ranked=5) What confuses me is that this code is data1 vs data2 or data2 vs data1.

The third question is that the input data is raw gene count matrix, but my single cell dataset is from several different studies. Whether the analysis of the raw gene count matrix takes into account and addresses batch effects effectively?

Looking forward to your reply very much.

Mengshu123 commented 1 year ago

I have knew that the following code:All_Markers[[i]]=scCODE(data1,data2,light = TRUE,top_ranked=5) is data1 vs data2, but I still confuses the first and third questions.