CSIDE results csv files all vs. sig

[meaksu]

Hi, I had a few questions about the raw data results when running CSIDE, as in run.CSIDE.single, for different cell types. This generates an "all_celltype.csv" file and "sig_celltype.csv" file for each cell type.

1. Is the p_val column the non-adjusted or adjusted p-value when keeping the default parameters i.e. Benjamini-Hochberg and fdr = 0.01?
2. What are the thresholds that include whether a gene is included in the "sig" csv file? Is this where the FDR test is applied if the p-value is listed unadjusted? For example in the "all" file some genes are < 0.01 pvalue but aren't included in the "sig" file.

Thank you

[dmcable]

Hello,

1. The p_val is unadjusted. We use q_val for the adjusted value.
2. Yes, this is where the FDR test is applied with a q-value threshold.

Best, Dylan