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Published 20 hours ago • verified publisher icon KlugerLab

Differential expression

Open DzenisKoca opened this issue 1 year ago • 5 comments

Hello,

First of all, thank you for this tool. ALRA seems really convincing and is performing really fast. I wanted to ask few questions regarding the use of ALRA. Data I am using contains 6 samples, from 6 different mice, 3 of wich are KO for certain gene. I want to compare 3 KO to 3 WT.

  1. Should ALRA be run on data that was normalized using Seurat's SCTransform() function?
  2. If I am using ALRA on few samples that I want to integrate using Seurat, is it ok to run ALRA on each sample individualy, before integration? I am using Seurat's SCTransform integration pipeline.
  3. After integration, can I use data imputed by ALRA to perform differential expression analysis?
  4. After integration, should I use some tool to remove batch effects between samples (3KO and 3WT individualy)?

DzenisKoca avatar Aug 19 '22 14:08 DzenisKoca