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In testing H 0 versus H 1, there are two types of errors that can be made: H 0 can be falsely accepted (miss detection) or H 0 can be falsely rejected (false alarm).
A largely used concept of error control in such multiple testing is the expected proportion of falsely rejected hypotheses, or False Discovery Rate (FDR).
Gene ontology analysis was performed for the functional categorization of differentially expressed genes using agriGO tool (http://bioinfo.cau.edu.cn/agriGO/), and the p-values were corrected by applying the false discovery rate correction to control falsely rejected hypothesis during the analysis.
To take into account the possibility of false-positive associations, the expected proportion of falsely rejected hypotheses will be controlled using a sequential Bonferroni-type procedure described by Benjamini and Hochberg.
This linear step-up approach controls the expected proportion of falsely rejected null hypotheses (i.e., the false discovery rate is expected to be no greater than 20%) and has some advantages (including more power) over Bonferroni-type procedures that control the family-wise error rate.
To control the proportion of falsely rejected null hypotheses among all 18793 tests (i.e., false discovery rate), raw p-values were adjusted using the Benjamini-Hochberg method [ 72].
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It can be calculated using parameters in contingency table using Eq. 1. Whereas, FPR also known as false alarm ratio refers to the probability of falsely rejecting the null hypothesis.
Similarly, the false-positive rate is the fraction of times we falsely reject the null hypothesis.
However, as the failure to reject a false chemical formula is arguably a lesser concern than falsely rejecting the true chemical formula, such a trade-off will in most cases be warranted.
However, applying the Bonferroni correction would be too stringent and might falsely reject true effects.
This form of study thus has some potential for type II error, falsely rejecting a useful drug.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com