I am trying to analyze a gene expression dataset with three treatments (A, B, and control). There should not be any interaction effect. I will be thankful to you if can briefly explain how to obtain differentially expressed genes under these conditions.
How can I define my reference for the expression analysis when I have three treatments? How can I define my formula?
is it ~ A + B?
when I show over-expressed genes, should I have two lists? e.g.,
A vs Control B vs Control
1 answer
Hi, you should have a single column in your metadata for condition, and this should contain A, B, and control.
For example:
metadata <- data.frame(
condition = c(
'A','A','A',
'B','B','B',
'control','control','control'))
metadata$condition <- factor(metadata$condition,
levels = c('control','A','B'))
So, your design formula would be:
~ condition
Then, you can compare different levels like this: DESeq2 compare all levels
Kevin
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