Applying Causal Discovery methods (CIT) on log transformed tpm data vs log transformed DESeq normalized data have differences why ?
0
0
Entering edit mode
8 months ago
rbiswas876 • 0

I wanted to understand whether gene length normalization has an effect on causal discovery methods. Suppose I have raw gene count and now I normalize it in two ways (1) by TPM (TPM normalizes by gene length also) and (2) by following DESeq2 scaling factors (DESeq don't account for gene length). So now I have two different normalized count data. Now I log2 transform both data and apply the causal DIscovery method (CIT Millstein, Joshua, et al. "Disentangling molecular relationships with a causal inference test." BMC genetics 10.1 (2009): 1-15.).

  1. Why I see differences in the causal relationship identified? Does scaling have an effect on Causal Discovery methods?
  2. How do I interpret the differences theoretically?
causal discovery DESeq CIT • 353 views
ADD COMMENT

Login before adding your answer.

Traffic: 2414 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6