Beruflich Dokumente
Kultur Dokumente
1/21/2010
Copyright 2010 Kun Liang
Plot Genotype B
150 100 50 0 Split Plot or Sub Plot
Genotype C
0 100 150 50
Genotype A
50 100 150 0
Block 2
Genotype B
150 100 50 0
Genotype A
0
Genotype C
50 150 0
Genotype A
Block 3
100 50 0 150
Genotype B
0 100 150 50
Genotype C
50 100 150 0
Genotype B
Block 4 0
Genotype C
50 0
Genotype A
50 150 100 0
2
Genotype is called the whole-plot factor because its levels are randomly assigned to whole plots.
Fertilizer is called the split-plot factor because its levels are randomly assigned to split plots within each whole plot.
3
Thus we have two different sizes of experimental units in split-plot experimental designs.
4
Block 2
Block 3
Block 4
1. There is equal interest in all treatment comparisons. 2. There is no natural way to group similar experimental units together in blocks.
3. No logistical constraints make complete randomization impractical.
7
1. Comparisons among the levels of the split-plot factor are greater interest than comparisons among the levels of the whole-plot factor.
2. Logistical constraints make a CRD or RCBD impractical.
9
Genotype C
0 100 150 50
Genotype A
50 100 150 0
Genotype B
150 100 50 0
Block 2
Genotype B
150 100 50 0
Genotype A
0
Genotype C
50 150 0
Genotype A
Block 3
100 50 0 150
Genotype B
0 100 150 50
Genotype C
50 100 150 0
Genotype B
Block 4 0
Genotype C
50 0
Genotype A
50 150 100 0
10
Block 1 B0
B50
B100
B150
C0
C50
C100
C150
Consider the same loop designs for blocks 2, 3, and 4 perhaps reversing loop directions for two of the four blocks.
12
Split-plot design structures dont necessarily involve plots in the usual sense. 1) Suppose a total of 8 horses are assigned to two diets (A and B) using a completely randomized design (CRD) with 4 horses per diet. 2) After 4 weeks on the assigned diet, each horse is sacrificed and RNA samples are taken from the stomach and small intestine of each horse. 3) Affymetrix GeneChips are used to measure gene expression in each RNA sample with one GeneChip for each of the samples.
13
organ RNA sample is playing the role of the split-plot experimental unit
14
Diet is the whole-plot factor with levels A and B. Organ type is the split-plot factor with levels stomach and small intestine.
15
Note that the levels of the factor diet are randomly assigned to experimental units. That is not the case for the levels of the factor organ type, but we will analyze it and refer to it just as we would have for an experimental factors whose levels are randomly assigned. 16
stomach
small intestine
stomach
small intestine
stomach
small intestine
stomach
small intestine
Diet B
Diet B
Diet B
Diet B
Connect samples of the same organ type between horses treated with different diets because this will give us the tightest comparison between diets for each organ type (and this is the comparison of primary interest). 18
Overview of lecture
1) 2) 3) 4) 5) 6) What is a split plot design Partitioning the variability Pre-analysis checks Example ANOVA Reporting the Results Summary of ANOVA
F ratios
For the main effects and the interaction there are separate F ratios calculated
FA MSA FB MSB MSS / A with (a 1) & (a )( s 1) df
MSBxS / A
FAB MS AB
MSBxS / A
Complete Example
Assessing a drug treatment to reduce systolic blood pressure
180 170 160 150 140 130 120 1 hour 5 hours 9 hours Drug Placebo
Pre-analysis checks
Homogeneity of Variance
For a mixed design it is necessary to check in a variety of different ways
Overall - Boxs M Within subjects - Mauchlys W Between groups - Levenes test
Normality
This can also be tested in a number of ways
Homogeneity of variance
Box's M F df1 df2 Sig. 4.189 .466 6 724.528 .834
TIME
Mauchly's W .535
df 2
Sig. .060
Levene's Test Blood Pressure (1 hr) Blood Pressure (5 hrs) Blood Pressure (9 hrs)
df1 1 1 1
df2 10 10 10
Normality
S.E. z p 0.845 -1.620 0.105 0.845 1.014 0.310 0.845 0.841 0.400 0.845 -0.370 0.711 0.845 -0.791 0.429 0.845 0.540 0.589
Anova Summary
Mixed Design (alias Split Plot)
Source of Variation
A (Treatment) 4761.000 1 4761.000 83.820 0.0000 B (Time) 2198.000 2 1099.000 32.324 0.0000 AB 1554.000 2 777.000 22.853 0.0000
*** ***
180 170 160 150 140 130 120 1 hour 5 hours 9 hours Drug Placebo
*** ***
180 170 160 150 140 130 120 1 hour 5 hours 9 hours Drug Placebo
Drug Placebo
Table 1: Means (and standard deviations) of blood pressure for the drug and placebo treatment groups for three times post adminstration
The simple main effect of time was significant for both the drug group (F2,20=51.235, MSE=34.000, p<0.001) and the placebo group (F2,20=3.941, MSE=34.000, p<0.05). Post hoc tukey tests (at p0.05) were conducted to explore further these effects. For the simple main effect of time for the drug group blood pressure was different between 1 hour and 9 hours and between 5 hours and 9 hours. However, blood pressure at 1 hour and 5 hours were not significantly different. Blood pressure was lower at 1 hour and 5 hours than at 9 hours for the drug group. For the placebo group, there was one significant difference between 1 hour and 5 hours with blood pressure at 5 hours being significantly greater
Summary of ANOVA
ANOVA is a parametric statistical technique for testing the differences between means. ANOVA can be used to analyse both single factor and multifactorial designs. Anova can be used to analyse differences in between ANOVA , within subjects and mixed designs.
Summary of ANOVA
A number of assumptions are made by ANOVA that should be tested prior to analysis Significant results often require further analysis Both planned and unplanned comparisons can be conducted Interactions nearly always require further analysis A failure to find a significant result may be due to lack of statistical power
Split-Plot Experiment
Top Shrinkage by Wool Fiber Treatment and Number of Drying Revolutions
J. Lindberg (1953). Relationship Between Various Surface Properties of Wool Fibers: Part II: Frictional Properties, Textile Research Journal, Vol. 23, pp. 225-237
Data Description
Experiment to Compare 4 Wool Fiber Treatments at 7 Dry Cycle Lengths over 4 Experimental Runs (Blocks) Response: Top Shrinkage of Fiber Restriction on Randomization: Within Each block, each treatment is assigned to whole plot, then measurements made at each of 7 dry cycle times (split plots) Whole Plot Treatments: Untreated, Alcoholic Potash (15 Sec, 4Min, 15Min) Subplot Treatments: Dry Cycle Revolutions (200 to 1400 by 200) Blocks: 4 Experimental Runs (possibly different days)
Block Layout
Revs 200 400 600 800 1000 1200 1400 200 400 600 800 1000 1200 1400 200 400 600 800 1000 1200 1400 200 400 600 800 1000 1200 1400
Trt A A A A A A A B B B B B B B C C C C C C C D D D D D D D
Whole Plot
Subplot
Marginal Means
run 1 2 3 4 average 23.63 24.77 22.48 22.07
trt 1 2 3 4 average 31.30 23.42 21.18 17.05
45
40
35
Shrinkage
25
20
15
10
0 0 200 400 600 800 Dryer Revolutions 1000 1200 1400 1600
Analysis of Variance
Source Treatments Blocks BlkxTrt (Error 1) Revs TrtxRevs Error 2 Total df 3 3 9 6 18 72 111 SS 3012.53 124.29 114.64 11051.78 269.51 99.16 14671.90 MS 1004.18 41.43 12.74 1841.96 14.97 1.38 F 78.84 P-Value 0.0000
1337.46 10.87
0.0000 0.0000
Note that there is a significant interaction (as well as main effects). Thus the profile relating shrinkage to # of revolutions differs by treatment
Decomposing the Revolution and Trt/Rev Interaction Sum of Squares into Polynomial Effects Note that for Revolutions, we have thus far treated these as nominal categories, however, it is a continuous variable We can break down its sums of squares into orthogonal polynomials representing linear, quadratic, cubic, components (6 in all) Graph appears to show at least linear and quadratic terms. Similar breakdown can be done on Treatment/Revolution interaction
The Revolution Main effect and the Treatment/Revolution Interaction is made up of significant linear and quadratic components
45
40
35
30
25
20
Shrinkage
15
10
Procedure for Obtaining Polynomial SS 1. Obtain coefficients for orthogonal polynomials from stat design or math source
Revs 200 400 600 800 1000 1200 1400 Linear -3 -2 -1 0 1 2 3 Quadratic 5 0 -3 -4 -3 0 5 Cubic -1 1 1 0 -1 -1 1 Quartic 3 -7 1 6 1 -7 3 Quintic -1 4 -5 0 5 -4 1 Sextic 1 -6 15 -20 15 -6 1
2. Obtain Linear Combinatio n of Means Across Revs L1 3 y 200 2 y 400 1y 600 0 y 800 1y1000 2 y1200 3 y1400 ... L6 1y 200 6 y 400 15 y 600 20 y 800 15 y1000 6 y1200 1y1400
(4)( 4) L2 6 Sextic : SS 6 (1) 2 (6) 2 (15) 2 (20) 2 (15) 2 (6) 2 (3) 2 Where the (4)(4) 16 in numerator represents the number of
This process can also be extended to the TreatmentxRev interaction by: 1) apply it within treatments (there are only 4 samples per Trt/Rev combination) 2) Sum each polynomial component over treatments and subtract results from 3)
Note the second and last rows (of the numeric values) give the polynomial sums of squares for the factors Rev, and Trt x Rev, respectively.