Corrections forMultiple Comparisons Hervé Abdi1 1 Overview The more tests we perform on a set of data, the more likely we are to reject the null hypothesis when it is true (i.e., a “Type I” error). Recently, adjustments for multiple tests (or Bonferroni adjustments) have found their way into introductory texts on medical statistics, which has increased their apparent legitimacy. It is a simple adjustment of the above Bonferroni method. However, this method hypothesizes that all experiments are independent and thus is considered to be overly conservative. This paper advances the view, widely held by epidemiologists, that Bonferroni adjustments are, at best, unnecessary and, at worst, deleterious to sound statistical inference. The Bonferroni correction tends to be a bit too conservative. stream The formula simply modifies the F-critical value by taking into account the number of groups being compared: (a –1) F crit. The second option is a Bonferroni correction (which we’ve encountered before), and the final option is a Sidak correction, which should be selected if you are concerned about the loss of power associated with Bonferroni corrected values. The Bonferroni correction sets the signicance cut-oat =n. Statistics 371 The Bonferroni Correction Fall 2002 Here is a clearer description of the Bonferroni procedure for multiple comparisons than what I rushed in class. Bonferroni correction for multiple testing is applied (the p-values in the ‘Sig’ column are multiplied by the number of tests being carried out to give the ‘Adj. <> %PDF-1.2 31 0 obj x��WMo�6zT���RQ�~3Ǡ���=�ٞ��ص;��?���7�(�^9��k`���pfޛ��c+��?��鮑"H�����Шh�Ю�Z���! 6 0 obj The most well known correction is called the Bonferroni correction, it consists in multiplying each prob- ability by the total number of tests performed. endobj The Bonferroni correction controls the number of false positives arising in each family by using a probability threshold of α/nfor each observation within the family. • Sacrifices slightly more power than TUKEY, but can be applied to any set of contrasts or linear combinations (useful in more situations than Tukey). To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. The most conservative multiple comparison is Bonferroni correction . Bonferroni correction, however, is well known to yield increasingly conservative pairwise comparison procedures as the number of samples to compare increases. The Bonferroni correction, named after the Italian statisti-cian Carlo Bonferroni (1892–1960), was based on a method proposed initially by Neyman and Pearson1 to aid decisions in studies involving repetitive sampling. H�x�Z���f(�Z"��R�A�a7��ӾA��RU�_@s ->Uk. endobj ��y.> ��%����9G����uLB�;��c�e�(D{56�@&fռr`�F���9щ���)+'���8QID�'�Ŷ����bK��j}:����%�� v_g�7�����ɻ��D��4�'�,���j���q[F���M^�G�u rI����* ��aU��ɒ&B�v����e�д8����d����4��!n��&�J���YRZ(�f_�w�c�hz�EL���^FLRU>�{�j��f�r�p���h���{�LѸq6gݺ�i�@vendstream Bonferroni Correction One of the most basic and historically most popular fixes to this problem is the Bonferroni correction. 16 0 obj This is a consequence of the logic of hypothesis testing: We reject the null hypothesis if we witness a rare event. In large univariate tests of all the pairwise SNP-QT associations, the p-value obtained from each single test is generally further corrected using various strategies. %�쏢 For example, in the example above, with 20 tests and = 0:05, you’d only reject a null hypothesis if the p-value is less than 0.0025. It basically multiplies each of the significance levels from the LSD test by the number of tests performed, i.e. Dni�>x�)��0�O �f��Y��JI�a� # of Comparisons = () 2 s s −1 The Bonferroni Comparison corrects for accumulating a errors by dividing by the number of comparisons being made. F�����%\ ���E�(e�H�iqFi�)�#�]����Q�q���zE�ɘ`���/2��b��R�qf�"|za�]p1 <> Bonferroni is generally known as the most conservative method to control the familywise error rate. Corrections forMultiple Comparisons Hervé Abdi1 1 Overview The more tests we perform on a set of data, the more likely we are to reject the null hypothesis when it is true (i.e., a “Type I” error). x��XKs5�8b�3���V�) The result is of course α = 1 − (1− P)1/k. endobj Basically, here are 2 ways of doing it and both lead to the same result: one way, as you did: when deviding threshold level (0.05) by number of tests. improvement over Bonferroni, while the permutation method offers substantial improvement over the random ” eld method for low smoothness and low degrees of freedom. Bonferroni. %�쏢 ƹ*[sV�~� Xx. stream Bonferroni’s correction Just take the formula P = 1 − (1− α)k and solve for α in terms of P, where usually P = 0.05. When deciding whether to accept or reject an individual null hypothesis, a probability threshold, α, is … <> PERMUTATION TESTING TO THE RESCUE! Such sequential corrections have increased power, as Example 4 below shows. J*(J-1)/2. 1�)���Ʃ�ڎp��{�43z�j�m�q�V�j����C���z����mǙ��:����Nx-�4��X&�w��[yÔ5�2ӜR�Y ��'�6�e����{�E�kL������u�:���m�jݽ8r�P�zݯ7]`]�?�e�s�q���m�n�e�L[ŕ����� ��`$����qř��3|Lԛ����0��'�T�7���u�+�*鿯�~Xwo'������*83F��F� ��LS'��P��a%�d�h�I"�͚s&�p6��$����� ��H Bonferroni correction is based only on the number of tests, instead of the information that can be found in the tests. This is a consequence of the logic of hypothesis testing: We reject the null hypothesis if we witness a rare event. 14 0 obj 607 stream But the larger the Whether or not to use the Bonferroni correction depends on the circumstances of the study. Sig). A randomised placebo controlled, double blind trial study design was used. We reject the null hypothesis if any of the tests reaches the tail probability α (i.e. ��J�c0���/�������qV�>;+N)��h��>�S4*D��'�r�p�(LGe̜�,$/����y�b��djr_u�ٙB�x9�:�d����%m���g�Y�|�6g�Ka�lٔ(H�����J*��!3�6W�xZ���CU�������9O\����:��%_��j�� 7 0 obj Bonferroni correction assumes that the tests are independent – which many EEG results are NOT 2. x��XKs5Nq���3+��*��`�PIX�C����İv�U�#�^�5�H�;k;Uį�{[��O�y#���;?��wJ�| ��W/;��Ɖ��Ҙ�y��N�w mSiQIo���w ͮ���F|씸�eU��~��E���y����ȏ���p�B��ъ�iǬ+�Q�{�J� PRi���I�`P�zTh��H�ч~3h �;ۿVJF�s��D�\�|1�tpR��'�J�B���f]��-���/ݽu�(T��ҿc�gZD�Ҳ�ɿ����S2���?�NV� �6� -edF�:S��烕h�F The Bonferroni correction compensates for that increase by testing each individual hypothesis at a significance level of /, where is the desired overall alpha level and is the number of hypotheses. It should not be used routinely and should be considered if: (1) a single test of the 'universal null hypothesis' (Ho ) that all tests are not significant is required, (2) it is imperative to avoid a type I er … When to use the Bonferroni correction Ophthalmic Physiol Opt. 9 A ‘Bonferroni correction’ is achieved by dividing the probability value (usually .05) by the number of tests conducted. endobj The Bonferroni correction, named after the Italian statisti-cian Carlo Bonferroni (1892–1960), was based on a method proposed initially by Neyman and Pearson1 to aid decisions in studies involving repetitive sampling. :a�+d�,�H�-DNJj_P�h� �ۇF����Q�͛�C���p^ �� �����}�i�B���Ѷ���U���{a�4-�RQ��5o�? Holm’s Method The simplest of these corrections is Holm’s method (Holm 1979). The Scheffe test computes a new critical value for an F test conducted when comparing two groups from the larger ANOVA (i.e., a correction for a standard t-test). Yes, for Bonferroni correction you did correct. Introduction Several biological, epidemiological and clinical studies have “time to an event” as their endpoint. Identical to the Bonferroni correction. # of Comparisons = () 2 s s −1 The Bonferroni … The Bonferroni adjustment is the simplest. �,=(��,6�ra���?�M�endstream VN���ޯ�L��Sw�A3�^��W;�HE�o�=�K��*� ��M��I�{��=�֮W�X��{p���^CJ� ��hC�8*Z"��� Identical to the Bonferroni correction. if the most For which of the following does the Bonferroni correction reduce the probability of occurring? {�X����"�����#�w�� �������J�(��=,>�A��2"Ax�h�v�2$�?���m��}p&���d�gG��tl~�qWw�C)�ov����S�'%(~sp��!I��ݏ��J �{�k��{? {�/z/�:�� �T�jB8� �9ʏ3+La&k�(�x�TVFa�"��`D��_��v\|��@5�SȠP��]�Z���磰�*�W�WE۫�^�[#>����\�X9�y������k,�=V��h5H�������oj���e+O�Z#0Z�h�z#�:K�Mߠ��q8}=M�^tH�ܳȎ�{� ��ny_�y2�)9UR%�I��E[ ����E��ẗ� �w�-0]���KpSc��^G����T~ZY��o�����a0��,��|N�R�rU�k�T�p�Q�o����� c��� Corrections “Bonferroni adjustments are, at best, unnecessary and, at worst, deleterious to sound statistical inference” Perneger (1998) •Counter-intuitive: interpretation of finding depends on the number of other tests performed •The general null hypothesis (that all the null hypotheses are true) is rarely of interest •High probability of type 2 errors, i.e. In order to adjust for them, I searched for a way in R and realized that implementing a multiple testing adjustment is easier than I thought/remembered. 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