Set default pval_threshold default to 0.05 and lfc threshold to 0

ByrumLab / proteoDA

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Set default pval_threshold default to 0.05 and lfc threshold to 0 #214

Closed tjthurman closed 1 year ago

tjthurman commented 1 year ago

For the public, the default pval threshold for significance should be 0.05, instead of the 0.055 we use internally. I'm a little torn on the default LFC to use: I think we should probably use 0 (since using a higher threshold value technically makes the p-value adjustment no longer correct).

ByrumLab commented 1 year ago

Leave the logFC default set to 1.