Dear DepMap community,
I would like to ask some more methodological/technical questions regarding the two-class comparison of custom analysis section; in detail, based on pre-defined groups of cancer cell lines, I noticed the following “differences” in the interpretation of results:
while using the CRISPR (DepMap 21Q4 Public, Chronos) dataset
and with the RNAi dataset:
The difference in the results, regarding the top hits and the profiling of included cell lines, is based in each methodological pipeline of scoring dependencies?
In addition, which is the main difference between the above CRISPR and the CRISPR (DepMap 21Q4 Public +Score, Chronos)? mainly on the profiled cell lines and the batch effect correction? And the latter corresponds in the downloads section in the CRISPR_gene_effect.csv file?
Regarding the statistical test implemented: as the two-group comparison uses empirical-Bayes moderated effect size estimates, regarding the hypothesis generation, could someone uses the raw p-values instead of Q-values? even with small effect sizes ?as it might be that including all the available genes, might result in stricter multiple correction?
Finally, when comparing Group 1 vs Group 2, a positive effect estimate would indicate, a higher essentiality in that gene in the second group?
Thank you in advance for your overall help and support