Dear list, I noticed a strange distribution of q values after correcting a list of 22960 p values with the q value package: > qsummary(q) Call: qvalue(p = p, robust = T) pi0: 0.07742146 Cumulative number of significant calls: <1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1 p-value 293 1067 3104 4634 7247 12082 22689 q-value 0 567 4901 17702 21382 22690 22690 As you can see, starting with a cutoff of < 0.01, the number of significant q values is higher than the number of significant p values, which, in my mind, should not be the case. The p value distribution looks ok (see attached histogram). I have also attached the q value plots and the p value vector for information. Any suggestions why these q values behave the way they do? Greetings Reinhard -- Dr. Reinhard Hoffmann Max-von-Pettenkofer-Institut Pettenkoferstr. 9a 80336 M?nchen Germany Phone: +49-89-5160-5424 (office), -5246 (Lab) Fax: +49-89-5160-5223 Mobile: +49-171-5169923 Email: r_hoffmann at mvp.uni-muenchen.de -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 8.0.1 - nicht f?r kommerzielle Nutzung lizenziert: www.pgp.com mQGiBEBiqn0RBADD7cwc5NHH98xZUn0hG53uL1nw2aVRXwurSWjqK5ytCUh2ZqB4 f/td9yCpQP3KYTzt4oW0wLK80OOvQ6twiozh49lcxWBGw4aY29RZADrV341MbJZm mcwp03VKaV++x+lEPepjUrIZQpYh5YMdnlFBMBF7J5jyS7LU22qbV+KwVwCg/8PI HO7/xBgu5JBYLP10O1sBSPkEAIZptRAYY4GO8hSX60Go8bSjLm/M/2lwYNqueSL/ AwYFR6OqCnBCAtjrv8YLB0puAso2GsSXJd6kjHDWBIzFaBwaPxNcIkYvbVycaByk zSvucM9EqR6fUzm4TDelCH+ISAeRa1gUOf9H1q7f0iPFKeaETSaPk2LX6QhJlnn/ /jfyBACOsbsZuM0uUGAbATa9ioS3ssQ8LVM0aiZaNUsEzsjb/8N7FPmKnqG5o1Aq PCIbk2Vk7f1IOZdJmBPXH70hLMJHHOyGmTBYFpscAUHMa7wlqJjVoVVu9On+Wa1u YnKWRrfdgSCIWc/x9JE6nKtAhykIeWTcuaOmQ+Z8qvz7/iGso7RARHIuIFJlaW5o YXJkIEhvZmZtYW5uIDxyX2hvZmZtYW5uQG0zNDAxLm1way5tZWQudW5pLW11ZW5j aGVuLmRlPokAWAQQEQIAGAUCQGKqfQgLCQgHAwIBCgIZAQUbAwAAAAAKCRDRdQPa E3rr/yoYAKDZn0r8AbkVwZCowvO4hyTbBSeuBQCfYdWSBK+UDk5oDBl/dHj9vz0L 6JC5Ag0EQGKqfRAIAPZCV7cIfwgXcqK61qlC8wXo+VMROU+28W65Szgg2gGnVqMU 6Y9AVfPQB8bLQ6mUrfdMZIZJ+AyDvWXpF9Sh01D49Vlf3HZSTz09jdvOmeFXklnN /biudE/F/Ha8g8VHMGHOfMlm/xX5u/2RXscBqtNbno2gpXI61Brwv0YAWCvl9Ij9 WE5J280gtJ3kkQc2azNsOA1FHQ98iLMcfFstjvbzySPAQ/ClWxiNjrtVjLhdONM0 /XwXV0OjHRhs3jMhLLUq/zzhsSlAGBGNfISnCnLWhsQDGcgHKXrKlQzZlp+r0ApQ mwJG0wg9ZqRdQZ+cfL2JSyIZJrqrol7DVekyCzsAAgIIAMQrT0Bic9AFu456+JXR qFT58G/mB/JSdvlbueq+8Sr0W4x7KdJ7uxKV+Iuk557pbAbP6WnBHeG3t0p0jCTr kAt4rLVAHS3Yz8j4M1q3K45TWFB0AjgKGVM8JvWlgYHWYRzSAMVMtjH+Jhr3SoBh 4ZnpmlWJ0rhKF7V4ioC4fOtz+BM3CnPyRi2effevIGbIM4zC4C0jxY6Hy9JecvJh 2j35D5gHiJWvHUXYCtdSBNLYDEmSmK5WuoEY7FjskyTd70wbM8lv+zwyKpq6kqnc XverpxyU49chB3Do9seEMWHZZTPfzKfJRHPIOCsjU3GTiQkbl1zDz1FgOZ4Xx539 dg6JAEwEGBECAAwFAkBiqn0FGwwAAAAACgkQ0XUD2hN66/8VDwCgq/2PAsRp0rAX iXS1T2bL7Fow9zUAnAtzantYb0tV+Iw603AsKQjyDPBW =LGSI -----END PGP PUBLIC KEY BLOCK----- -------------- next part -------------- A non-text attachment was scrubbed... Name: ANOVA_p.png Type: image/png Size: 4036 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20051102 /9c2d907a/ANOVA_p.png -------------- next part -------------- A non-text attachment was scrubbed... Name: qplot.png Type: image/png Size: 7638 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20051102 /9c2d907a/qplot.png