ANALYSIS QUESTIONS

[Athanasios-Dimitrios Bakasis]

Hi, 

I tried to use PinAPL and compare the various processing and analysis methods available (which are great) compared to MaGeck.

1) Fold change difference between treatment/controls in an enrichment experiment is calculated with the negative binomial method while p value adj can  be calculated with either sidak or fdr-bn or bonf? because i have analyzez my data (3 treatment, 3 controls) and and while i get different p values for sgRNA ranking between sidak and fdr-bd (as expected) i also get different fold changes...why is that?

2) Is there a way to find out the FDR for our analyses as displayed a few years ago at the CRISPR screening Workshop?

3) If p value is less than 0.01 how isignificance can either be TRUE or in other sgRNAs FALSE?

Thank you in advance!
Sincerely, 

Athanasios