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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.
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?
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
The text was updated successfully, but these errors were encountered:
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.
Thank you
The text was updated successfully, but these errors were encountered: