Hi,
The log2 fold change is calculated as log2 (treat)/(control). In the factor level section, is ‘1: Factor level’ a denominator and ‘2: Factor level’ is a numerator?
Galaxy’s DESeq2 both states “Specify a factor level, typical values could be ‘tumor’,‘normal’,‘treated’ or ‘control’”, which is a bit confusing.
If the order is changed, the opposite result will come out, so I think everyone should pay attention to this part.
Hi,
in Galaxy, factor level 1 is considered the treated condition (numerator), and factor level 2 is considered the control condition. Indeed it can be a bit confusing; thanks for your feedback, it will be reported in order to clarify it.
Thank you for answer.
I want to be of some help to the Galaxy.
Galaxy is a really nice platform!
It sounds great! I recommend you to have a look at the Contributing to the Galaxy Training Material tutorials; probably there you can find additional ways for contributing.
Best regards.