Question for batch effect from input data

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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Question for batch effect from input data #159

Closed lh12565 closed 3 years ago

lh12565 commented 4 years ago

Hi,

I found the input of SCENIC is a count matrix. However, I have some samples with batch effect and can I use the directly merged count matrix as input? If not, I tried to run each sample individually, but the output is different, such as LEF1 (101g) for one sample and LEF1_extend (1034g) for another. How do I integrate it after that? Thanks!

s-aibar commented 3 years ago

Dear @lh12565 :

You can use the batch-corrected matrix as input to SCENIC. It will indeed provide different results than running it on each sample individually, but the interpretation, and how to merge the networks depends on your specific dataset...