Description of the bug
Hi
I have two biological replicates of two samples and this is my contrast file
reference;treatment
Day0_1,Day0_2;Untreated_1,Untreated_2
When I perform the analysis with nf-core/crisprseq (2.4.0dev), BAGEL2 calculates fold change by using reference column Day0_1 (not Day0_2). But if I do this analysis with nf-core/crisprseq (2.3.0), the fold changes are instead calculated using the mean of Day0_1 and Day0_2 as the reference.
Many thanks,
Command used and terminal output
Relevant files
No response
System information
No response
Description of the bug
Hi
I have two biological replicates of two samples and this is my contrast file
When I perform the analysis with nf-core/crisprseq (2.4.0dev), BAGEL2 calculates fold change by using reference column Day0_1 (not Day0_2). But if I do this analysis with nf-core/crisprseq (2.3.0), the fold changes are instead calculated using the mean of Day0_1 and Day0_2 as the reference.
Many thanks,
Command used and terminal output
Relevant files
No response
System information
No response