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Date:         Wed, 19 Jan 2011 17:33:48 -0500
Reply-To:     R B <ryan.andrew.black@gmail.com>
Sender:       "SPSSX(r) Discussion" <SPSSX-L@LISTSERV.UGA.EDU>
From:         R B <ryan.andrew.black@gmail.com>
Subject:      Re: Bonferroni correction and number of comparisons
In-Reply-To:  <1295473645731-3348646.post@n5.nabble.com>
Content-Type: text/plain; charset=ISO-8859-1

Bruce,

See a couple of comments interspersed below.

On Wed, Jan 19, 2011 at 4:47 PM, Bruce Weaver <bruce.weaver@hotmail.com> wrote: > Ryan, multiplying the observed (uncorrected) p-values by the number of > contrasts can give you results that make no sense. E.g., if the uncorrected > p-value = .25 and the number of contrasts is 6, you'll get a corrected > p-value = 1.5. But p-values are conditional probabilities, and must fall > within the range 0-1.

This is a valid point, but I've yet to encounter a situation in my work where I would've made a different conclusion by correcting alpha directly.

> > Here's an example using oneway ANOVA. Notice that the Bonferroni-corrected > p-values (or Sig. values as SPSS labels them) are not simply 3 x the > uncorrected (LSD) p-values.

I disagree. In your example, Bonferroni corrected p values associated with 1v2 and 1v3 are exactly the same uncorrected p-values times 3. Is there something I'm missing here?

My guess is that SPSS automatically replaced the Bonferroni corrected p-value associated with 2v3 with 1.0, since as you pointed out the conditional probability cannot be above 1.0.

> > MATRIX DATA VARIABLES=Group ROWTYPE_ Score /FACTORS=Group. > BEGIN DATA > 1 N 96 > 2 N 96 > 3 N 96 > 1 MEAN 22.98 > 2 MEAN 25.78 > 3 MEAN 26.56 > 1 STDDEV 8.79 > 2 STDDEV 9.08 > 3 STDDEV 8.50 > END DATA. > > ONEWAY Score BY group / > matrix = in(*) / > POSTHOC=LSD BONFERRONI ALPHA(0.05) > . > > Jan, given that figuring out how to compute corrected p-values may be quite > time-consuming, I would see if I could persuade the person who asked that > the usual approach (i.e., comparing p to a corrected alpha level) is > sufficient. > > HTH. > > > > R B wrote: >> >> You asked about applying a Bonferroni correction in post hoc tests--> >> "Is the Bonferroni adjustment for 6 comparisons and the corrected >> p-value (.05/6=.008333)" >> >> Answer. No. You have presumably adjusted the alpha level, not the >> p-values. Multiply the each p-value by the number of post hoc tests >> performed (6 in the example you provided). Then compare the adjusted >> p-values to the alpha level you set (e.g., .05). >> >> Ryan >> >> On Wed, Jan 19, 2011 at 1:56 PM, J McClure <mc006@pacbell.net> wrote: >>> Hi, >>> I am doing a post hoc analysis comparing column proportions and >>> adjusting (Bonferroni) for multiple comparisons (CTables, test >>> statistics option). >>> I've been asked to provide the corrected p-value. >>> I'd like to know if I am correct in reporting the corrected value as >>> .008. >>> The row variable has two levels (yes and no) and the column variable has >>> 4 levels, so I am making 6 comparisons for 'no' and 6 for 'yes'. >>> n*(n-1)/2 >>> The output shows the comparison for the 'no' and for the yes level of >>> the row variable. Is the Bonferroni adjustment for 6 comparisons and the >>> corrected p-value (.05/6=.008333) >>> Also, I have 19 row variables for which I am running column proportion >>> comparisons. I think that the comparisons for each of the 19 variables >>> are considered independent from each other so no further adjustment is >>> made by SPSS. Is this the way reviewers look at the question? >>> Thanks for any help, >>> Jan >>> >>> ===================== >>> To manage your subscription to SPSSX-L, send a message to >>> LISTSERV@LISTSERV.UGA.EDU (not to SPSSX-L), with no body text except the >>> command. To leave the list, send the command >>> SIGNOFF SPSSX-L >>> For a list of commands to manage subscriptions, send the command >>> INFO REFCARD >>> >> >> ===================== >> To manage your subscription to SPSSX-L, send a message to >> LISTSERV@LISTSERV.UGA.EDU (not to SPSSX-L), with no body text except the >> command. To leave the list, send the command >> SIGNOFF SPSSX-L >> For a list of commands to manage subscriptions, send the command >> INFO REFCARD >> >> > > > ----- > -- > Bruce Weaver > bweaver@lakeheadu.ca > http://sites.google.com/a/lakeheadu.ca/bweaver/ > > "When all else fails, RTFM." > > NOTE: My Hotmail account is not monitored regularly. > To send me an e-mail, please use the address shown above. > > -- > View this message in context: http://spssx-discussion.1045642.n5.nabble.com/Bonferroni-correction-and-number-of-comparisons-tp3348337p3348646.html > Sent from the SPSSX Discussion mailing list archive at Nabble.com. > > ===================== > To manage your subscription to SPSSX-L, send a message to > LISTSERV@LISTSERV.UGA.EDU (not to SPSSX-L), with no body text except the > command. To leave the list, send the command > SIGNOFF SPSSX-L > For a list of commands to manage subscriptions, send the command > INFO REFCARD >

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