I am working on a CRISPR data set and have run the
mageckFlute workflow with the MLE algorithm.
But I am not sure how to interpret the nine-square plot created by the
From reading the paper it somehow means, the genes in color shows a difference between the control and the treamment. But what does it mean here?
I have control samples from day 0, control samples from day 7 and treated samples from day 7.
my design matrix was as such:
sampleName baseline d7ctrl d7sen d0ctrl1 1 0 0 d0ctrl2 1 0 0 d0ctrl3 1 0 0 d7ctrl1 1 1 0 d7ctrl2 1 1 0 d7ctrl3 1 1 0 d7sen1 1 0 1 d7sen2 1 0 1 d7sen3 1 0 1
I compared my control and treatment after seven days against my day 0 samples.
Now, how can I interpret the purple genes? Are these genes the ones which show the highest difference between my treatment and my day 0 samples?
BTW, can this be done without mageck-VISPR? Can I use the normal
mageck mle output for this analysis?