# MEAN SEPARATION TESTS (LSD AND Tukey s Procedure) is rejected, we need a method to determine which means are significantly different from the others.

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1 MEAN SEPARATION TESTS (LSD AND Tukey s Procedure) If Ho n is rejected, we need a method to determine which means are significantly different from the others. We ll look at three separation tests during the semester: 1. F-protected least significant difference (F-protected LSD) 2. Tukey s Procedure 3. Orthogonal linear contrasts (covered at the end of the semester) F-protected Least Significant Difference The LSD we will use is called an F-protected LSD because it is calculated and used only when H o is rejected. Sometimes when one fails to reject H o and an LSD is calculated, the LSD will wrongly suggest that there are significant differences between treatment means. To prevent against this conflict, we calculate the LSD only when H o is rejected. LSD t and df for t = Error df / 2 * s Y 1Y 2 If r 1 r2... rn then s Y Y 1 2 2ErrorMS r If ri r i ' then s Y1Y s ri ri ' If the difference between two treatment means is greater than the LSD, then those treatment means are significantly different at the 1 % level of confidence.

2 Example Given an experiment analyzed as a CRD that has 7 treatments and 4 replicates with the following analysis SOV Df SS MS F Treatment 6 5,587, , ** Error 21 1,990,238 94,773 Total 27 7,577,412 and the following treatment means Treatment Mean A 2,127 B 2,678 C 2,552 D 2,128 E 1,796 F 1,681 G 1,316 Calculate the LSD and show what means are significantly different at the 95% level of confidence. Step 1. Calculate the LSD LSD t / 2 * s Y Y ErrorMS r (94,773)

3 Step 2. Rank treatment means from low to high Treatment Mean G 1,316 F 1,681 E 1,796 A 2,127 D 2,128 C 2,552 B 2,678 Step 3. Calculate differences between treatment means to determine which ones are significantly different from each other. If the difference between two treatment means is greater than the LSD, then those treatment means are significantly different at the 95% level of confidence. Treatment F vs. Treatment G = 365 ns Treatment E vs. Treatment G = 480 * Since E is significantly greater than Treatment G, then the rest of the means greater than that of Treatment E also are significantly different than Treatment G. Thus there is no need to keep comparing the difference between the mean of Treatment G and Treatments with means greater than the mean of Treatment E. Treatment E vs. Treatment F = 115 ns Treatment A vs. Treatment F = 446 ns Treatment D vs. Treatment F = 447 ns Treatment C vs. Treatment F = 871 * *Therefore Treatment B must also be different from Treatment F Treatment A vs. Treatment E = 331 ns Treatment D vs. Treatment E = 332 ns Treatment C vs. Treatment E = 756 * *Therefore Treatment B must also be different from Treatment E Treatment D vs. Treatment A = 1 ns Treatment C vs. Treatment A = 425 ns Treatment B vs. Treatment A = 551 *

4 Treatment C vs. Treatment D = 424 ns Treatment B vs. Treatment D = 550 * Treatment B vs. Treatment C = 126 ns Step 4. Place lowercase letters behind treatment means to show which treatments are significantly different. Step 4.1. Write letters horizontally G F E A D C B Step 4.2. Under line treatments that are not significantly different. G F E A D C B Step 4.3. Ignore those lines that fall within the boundary of another line. G F E A D C B Step 4.4 Label each line, beginning with the top one, with lowercase letters beginning with a. G F E A D C B a b c d Step 4.5 Add lowercase letters behind the respective means. Treatment Mean G 1,316 a F 1,681 ab E 1,796 b A 2,127 bc D 2,128 bc C 2,552 cd B 2,678 d

5 F-protected LSD when r j r j / LSD t.05/ 2; errordf s 2 1 rj 1 ' r j Given: SOV Df SS MS F Treatment ** Error Total And Treatment n Mean A B C D How man LSD s do we need to calculate? Step 1. Calculate the LSD s. LSD #1) Treatment A or C vs. Treatment B: LSD #2) Treatment A or C vs. Treatment D: LSD #3) Treatment A vs. C: LSD #4) Treatment B vs. D:

6 Step 2. Write down the means in order from low to high. Treatment n Mean B A D C Step 3. Calculate differences between treatment means to determine which ones are significantly different from each other. If the difference between two treatment means is greater than the LSD, then those treatment means are significantly different at the 95% level of confidence. Treatment A vs. Treatment B (LSD #1) = 0.3 ns Treatment D vs. Treatment B (LSD #4) = 0.4 ns Treatment C vs. Treatment B (LSD #1) = 0.7 * Treatment D vs. Treatment A (LSD #2) = 0.1 ns Treatment C vs. Treatment A (LSD #3) = 0.4 * Treatment C vs. Treatment D (LSD #2) = 0.3 ns Step 4. Place lowercase letters behind treatment means to show which treatments are significantly different. Step 4.1. Write letters horizontally B A D C Step 4.2. Under line treatments that are not significantly different. B A D C Step 4.3. Ignore those lines that fall within the boundary of another line. B A D C

7 Step 4.4 Label each line, beginning with the top one, with lowercase letters beginning with a. a B A D C b Step 4.5 Add lowercase letters behind the respective means. Treatment n Mean B a A a D ab C b F-protected LSD with Sampling when r j s k r j s k or r j s k =r j s k LSD t.05/ 2; errordf 2 1 s rjsk r 1 ' s j k ' If r j s k =r i s k : LSD t.05/ 2; errordf 2s rs 2 Tukey s Procedure This test takes into consideration the number of means involved in the comparison. Tukey s procedure uses the distribution of the studentized range statistic. q y max y min MS Error r Where ymax and ymin are the largest and smallest treatment means, respectively, out of a group of p treatment means. Appendix Table VII, pages 621 and 622, contains values of q ( p, f ), the upper α percentage points of q where f is the number of degrees of freedom associated with the Mean Square Error.

8

9 As the number of means involved in a comparison increases, the studentized range statistic increases. The basis behind Tukey s Procedure is that in general, as the number of means involved in a test increases, the smaller or less likely is the probability that they will be alike (i.e. the probability of detecting differences increases). Tukey s Procedure accounts for this fact by increasing the studentized range statistic as the number of treatments (p) increases, such that the probability that the means will be alike remains the same. MS Error If r i = r i, Tukey s statistic = T q ( p, f ) r Two treatments means are considered significantly different if the different between their means is greater than T α. Example (using the same data previously used for the LSD example) Given an experiment analyzed as a CRD that has 7 treatments and 4 replicates with the following analysis SOV Df SS MS F Treatment 6 5,587, , ** Error 21 1,990,238 94,773 Total 27 7,577,412 and the following treatment means Treatment Mean A 2,127 B 2,678 C 2,552 D 2,128 E 1,796 F 1,681 G 1,316 Calculate used Tukey s procedure to show what means are significantly different at the 95% level of confidence.

10 Step 1. Calculate Tukey s statistic. T T 0.05 q q ( p, f ) 0.05 (7,21) 23, MS Error r 94,773 4 Step 2. Rank treatment means from low to high Treatment Mean G 1,316 F 1,681 E 1,796 A 2,127 D 2,128 C 2,552 B 2,678 Step 3. Calculate differences between treatment means to determine which ones are significantly different from each other. If the difference between two treatment means is greater than T α, then those treatment means are significantly different at the 95% level of confidence. Treatment F vs. Treatment G = 365 ns Treatment E vs. Treatment G = 480 ns Treatment A vs. Treatment G = 811 * Since A is significantly greater than Treatment G, then the rest of the means greater than that of Treatment A also are significantly different than Treatment G. Thus there is no need to keep comparing the difference between the mean of Treatment G and Treatments with means greater than the mean of Treatment A. Treatment E vs. Treatment F = 115 ns Treatment A vs. Treatment F = 446 ns Treatment D vs. Treatment F = 447 ns Treatment C vs. Treatment F = 871 * *Therefore Treatment B must also be different from Treatment F

11 Treatment A vs. Treatment E = 331 ns Treatment D vs. Treatment E = 332 ns Treatment C vs. Treatment E = 756 * *Therefore Treatment B must also be different from Treatment E Treatment D vs. Treatment A = 1 ns Treatment C vs. Treatment A = 425 ns Treatment B vs. Treatment A = 551 ns Step 4. Place lowercase letters behind treatment means to show which treatments are significantly different. Step 4.1. Write letters horizontally G F E A D C B Step 4.2. Under line treatments that are not significantly different. G F E A D C B Step 4.3. Ignore those lines that fall within the boundary of another line. G F E A D C B Step 4.4 Label each line, beginning with the top one, with lowercase letters beginning with a. G F E A D C B a b c

12 Step 4.5 Add lowercase letters behind the respective means. Treatment Mean G 1,316 a F 1,681 ab E 1,796 ab A 2,127 bc D 2,128 bc C 2,552 c B 2,678 c Tukey-Kramer Procedure Used for unbalanced data (i.e., ri r i ' ). T q p, f Error MS ri r i ' Example Given: SOV Df SS MS F Treatment ** Error Total And Treatment n Mean A B C D How man T α values do we need to calculate?

13 Step 1. Calculate the T α values. Where T q p, f Error MS ri r i ' And q α (p,f) = q 0.05 (4,13) = T #1) Treatment A or C vs. Treatment B: T #2) Treatment A or C vs. Treatment D: T #3) Treatment A vs. C: T #4) Treatment B vs. D: Step 2. Write down the means in order from low to high. Treatment n Mean B A D C Step 3. Calculate differences between treatment means to determine which ones are significantly different from each other. If the difference between two treatment means is greater than the T -value, then those treatment means are significantly different at the 95% level of confidence. Treatment A vs. Treatment B (T α value #1) = 0.3 ns Treatment D vs. Treatment B (T α value #4) = 0.4 ns Treatment C vs. Treatment B (T α value #1) = 0.7 *

14 Treatment D vs. Treatment A (T α value #2) = 0.1 ns Treatment C vs. Treatment A (T α value #3) = 0.4 ns Step 4. Place lowercase letters behind treatment means to show which treatments are significantly different. Step 4.1. Write letters horizontally B A D C Step 4.2. Under line treatments that are not significantly different. B A D C Step 4.3. Ignore those lines that fall within the boundary of another line. B A D C Step 4.4 Label each line, beginning with the top one, with lowercase letters beginning with a. a B A D C b Step 4.5 Add lowercase letters behind the respective means. Treatment n Mean B a A ab D ab C b Tukey s Procedure with Sampling 2 q ( p, f ) s where s Y Y rs T * s

15 Tukey Kramer Procedure with Sampling T q ( p, f ) 2 1 s rjsk r s 2 1 j k '

16 Output of the Proc Anova Command The ANOVA Procedure Class Level Information Class Levels Values trt 3 a b c Number of Observations Read 12 Number of Observations Used 12

17 Output of the Proc Anova Command The ANOVA Procedure Dependent Variable: yield Source DF Sum of Squares Mean Square F Value Pr > F Model Error Corrected Total R-Square Coeff Var Root MSE yield Mean Source DF Anova SS Mean Square F Value Pr > F trt

18 Output of the Proc Anova Command The ANOVA Procedure

19 Output of the Proc Anova Command The ANOVA Procedure t Tests (LSD) for yield NoteThis test controls the Type I comparisonwise error rate, not the : experimentwise error rate. Alpha 0.05 Error Degrees of Freedom 9 Error Mean Square Critical Value of t Least Significant Difference Means with the same letter are not significantly different. t Grouping Mean N trt A c A B A b B B a

20 Output of the Proc Anova Command The ANOVA Procedure Tukey's Studentized Range (HSD) Test for yield NoteThis test controls the Type I experimentwise error rate, but it generally has a higher Type II error : rate than REGWQ. Alpha 0.05 Error Degrees of Freedom 9 Error Mean Square Critical Value of Studentized Range Minimum Significant Difference Means with the same letter are not significantly different. Tukey Grouping Mean N trt A c A A b A A a

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