Entering edit mode
4 months ago
Pallondyle
•
0
I'm trying to recurrent the FDR-Zscore dot plot in this article: Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection, figure 1.B I used the MaGeck sgRNA test data as my input (DIFF):
plot_dat <- DIFF %>%mutate(z_score = (LFC- mean(LFC)) / sd(LFC))
plot_dat <- plot_dat %>% mutate(fdr=ifelse(`pos.fdr`<`neg.fdr`,`pos.fdr`,`neg.fdr`))
plot_nont<-plot_dat[which(plot_dat$Gene=="Non-Targeting Control"),]
ggplot(plot_dat,aes(x=z_score,y=-log10(FDR)))+geom_point()+
geom_point(data=plot_nont,color="red")+
scale_y_continuous(limits=c(0,5))
and my plot is like this. I want to know what causes my data distributed like this. Is there any problem with my raw data?
Nobody can tell you. Did you run the exact same code they published? Same normalization? I don't see how people could help here, we cannot magically see your screen or the code from whatever paper this is.