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Ideally, for this test we would have the same number of replicates for each
treatment, but this is not essential. Advanced computer programmes can
overcome the problem of unequal replicates by entering "missing values".
1 12 20 40
2 15 19 35
3 9 23 42
Step 2. For each column, enter S x, n, , S x2, and Sd2 (click here for
method)
Step 3. [A check for equal variance - the underlying assumption of this test]
For each column divide Sd2 by n-1 to obtain the variance, s 2. Divide the
highest value of s2 by the lowest value of s 2 to obtain a variance ratio (F).
Then look up a table of Fmax for the number of treatments in our table of data
and the degrees of freedom (number of replicates per treatment -1). If our
variance ratio does not exceed the Fmax value then we are safe to proceed. If
not, the data might need to be transformed.
Step 5. Sum all the values for and call the sum B.
Step 6. Sum all the values for S x to obtain the grand total.
Step 7. Square the grand total and divide it by total number of observations;
call this D.
[The total df is always one fewer than the total number of data entries]
Step 12. Using the mean squares in the final column of this table, do a
variance ratio test to obtain an F value:
Step 13. Go to a table of F (p = 0.05) and read off the value where n1 is the df of
the between treatments mean square and n2 is df of the residual mean square.
If the calculated F value exceeds the tabulated value there is significant
difference between treatments. If so, then look at the tabulated F values for p
= 0.01 and then 0.001, to see if the treatment differences are more highly
significant.
If you look at many of the steps above they should remind you of the steps in a
Fmax test: F = 13/4.35 = 2.99. This is lower than the Fmax of 87.5 (for 3
treatments and 2 df, at p = 0.05) so the variances are homogeneous and we can
proceed with analysis of variance. If our value exceeded the tabulated Fmax
then we would need to transform the data.
Between-treatments S of S = B - D = 1140.2
Residual S of S = A - B = 52.7
[* For u treatments (3 in our case) and v replicates (3 in our case); the total df
is one fewer than the total number of data values in the table (9 values in our
case)]
The Analysis of Variance has told us only that there are differences between
treatments in the experiment as a whole. Sometimes this information is useful
in its own right. But it does not tell us which treatments differ from one
another.
We now have a problem, because every time we compare one treatment with
another (for example, comparing bacterium A with bacterium B) we are doing
the equivalent of a t-test, with a probability of making a wrong interpretation.
We need some way of avoiding this problem.
Method 1. Calculate the least significant difference between any two means.
[This is not generally favoured, but it can be used with caution.]
We make use of the fact that our calculations for Analysis of Variance were
similar to those of a t-test (see earlier); in particular, the residual mean
square is an estimate of s2 for each treatment, because the variance for all
treatments is assumed to be equal in an Analysis of Variance.
If we did this for two particular means,we could compare the calculated t with
that in a t-table, using the df of the residual mean square (because this
reflects the residual variance in the whole experiment).
In other words, any two means would be significantly different from one
another if they differ by more than "t multiplied by sd"
So t(sd) represents the least significant difference (LSD) between any two
means.
2 20.7
3 39
5% LSD 5.92
Here the author would be giving us the means for the 3 treatments (bacteria)
and telling us that analysis of variance was used to find the least significant
difference between any of the means at p = 0.05 (the level of probability
chosen for the t value).
In fact, the table above uses the data for bacterial biomass in our worked
example.
For 5% LSD, we find sd2 (= 2 x residual mean square / n). It is 17.56 /3 = 5.85.
Method 2. Many people now use variants of the LSD, such as a Multiple Range
Test, which enables us more safely to compare any treatments in a table. This
test is far preferable to the LSD. It is explained separately on another page.
Having entered the data on the spreadsheet, we select Anova: single factor
from the analysis tools, click OK, and enter all 9 cells of data in Input variable
range. The table shows the source of variance as "Between groups" (= between
treatments) and "within groups" (= residual). We are also told the calculated F
value (64.949..), the F value that we would need to exceed (F critical) in order
to have a significant difference between treatments, and the probability (p-
value) that our calculated F value would be obtained by chance (random
error) alone. This probability is very small (8.61 x 10-5) so we have a highly
significant difference between treatments in our table. We could then use the
residual (within groups) mean square (MS) to calculate LSD, as explained
earlier.
CONTENTS
INTRODUCTION
THE SCIENTIFIC METHOD
Experimental design
Designing experiments with statistics in mind
Common statistical terms
Descriptive statistics: standard deviation, standard error, confidence
intervals of mean.
STATISTICAL TESTS:
Student's t-test for comparing the means of two samples
Paired-samples test. (like a t-test, but used when data can be paired)
Analysis of variance for comparing means of three or more samples:
For comparing separate treatments (One-way ANOVA)
Calculating the Least Significant Difference between means
Using a Multiple Range Test for comparing means
For factorial combinations of treatments (Two-way ANOVA)
linear regression
logarithmic and sigmoid curves
STATISTICAL TABLES:
t (Student's t-test)
F, p = 0.05 (Analysis of Variance)
F, p = 0.01 (Analysis of Variance)
F, p = 0.001 (Analysis of Variance)
c2 (chi squared)
r (correlation coefficient)
Q (Multiple Range test)
Fmax (test for homogeneity of variance)