H + T = 1. p(h + T) = p(h) x p(t)

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2 p2 + 2pq + q2 = p + q (p + q) 2 = p 2 + 2pq + q 2 This is essentially an expression of the binomial expansion. The binomial expansion is represented as (p + q) n where p and q represent the probabilities of alternative, mutually exclusive events (probability of heads vs tails, boy vs girl, wild-type vs mutant allele, etc), and n represents the size of the group or the number of trials. Thus: 1 coin = (p + q) 2 coins = (p + q) 2 3 coins = (p + q) 3 4 coins = (p + q) 4 5 coin s = (p + q) 5 In the case of 3 coins, each (p + q) represents one of the coins and the probability of it landing heads vs tails. If we expand the 3 coin case, then the binomial expansion becomes: p 3 + 3p 2 q + 3 pq 2 + q 3 Each expression in the expansion is the probability of one of the possible mutually exclusive outcome: p3 = probability of three heads 3p 2 q = probability of two heads and 1 tail 3 pq2 = probability of 1 head and 2 tails q3 = probability of 3 tails The 3 s in two of the expressions indicate how many possible ways one can obtain two heads and 1 tail.. As the number of independent events increases, the binomial expansion can become extremely complex. Individual outcomes can be calculated by the equation: P = n! x!(n-x)! p x q (n-x) where n = the total number in the group and x = the number one one class. p = the probability of x occurring and q = probability of the other event occurring. For example, if 10 babies were born in a hospital one evening and you wanted to calculate the probability of 6 girls and 4 boys occurring, the n = 10 babies, x = 6 girls, and (n - x) = 4 boys. p = probability of a girl (0.5) and q = probability of a boy (0.5) Toss n coins 60 times and record the results the tables in the lab report where: # coins Table Use the binomial expansion to determine the expected values. The Chi-Square Test

3 X 2 is a test to determine the goodness of fit of experimentally derived data to a theoretical expected ratio. In the previous exercises we measured the deviations (observed - expected). Now we must make a judgement as to whether the deviations from expected values are small enough to occur by chance alone, or are large enough to disprove our working hypothesis. From the measured deviations, we can calculate the value X 2, which is a measure of the total deviation in the entire experiment. The formula for X 2 is: X 2 = (observed - expected) 2 expected X 2 is usually calculaed in table form. Once the X 2 value for an experiment has been calculated, it must be evaluated by comparison with a table of X 2 values. In order to use the X 2 test properly, one must understand exactly what is being evaluated. The X 2 test is always phrased in terms of the Null Hypothesis (Ho), which states: there is no significant difference between observed and expected results. It makes no difference what the original hypothesis was. The X 2 test is used only to determine whether or not the observed results are statistically the same as the expected. Acceptance or rejection of Ho then gives us a handle by which to evaluate the theory being tested by the experiment. For example, suppose two genes are believed to be unlinked. If this is indeed the case, a dihybrid cross should result in a ratio among the F2 progeny. The cross is performed and the expected results are calculated based on that ratio, based on the assumption of non-linkage. The actual results are then campared to the expected by the X 2 test. If the test leads us to reject the Ho, that the observed and expected results are different, then we must conclude that the hypothesis that enabled us calculate the expected values is, in fact, incorrect. If, on the other hand, if we accept the Ho, then we can conclude that the results are consistent with our hypothesis that the two genes are unlinked. It doesn t necessarily prove our hypothesis, but it gives us greater confidence that we are on the right track. To evaluate the Ho, the experimental X 2 value must be compared with a critical X 2 value from the table below. To find the appropriate critical X 2 value, we must know the degrees of freedom for the experiment, and the confidence level or probability. Degrees of Freedom: In each experiment, there is a fixed quantity of individuals divided up among the several classes of data. If there are 1600 individuals divided over only two classes, tall and short, for example, once the number of tall individuals are counted, the number of short individuals is fixed. If there are four classes, AB = 900, Ab = 300, and ab = 300, then the class ab must be 100. It makes no difference which classes we consider to be free and which is fixed. The important thing is that among four classes of data, three are free and one is fixed. Degrees of freedom is easily calculated because: degrees of freedom = # classes of data - 1. In the dihybrid cross example, means that there are 4 classes of data, so degrees of freedom would be 4-1 = 3 Thus the critical X 2 value would be found in the row for 3 degrees of freedom. Probability: If one repeats an experiment numerous times, the results will not be identical, but rather will vary around a mean. Likewise, it would be too much to expect that the expected results of a new experiment be exactly identical to the expected results. The X 2 value is a measure of the overall discrepancy in the experiment among all the classes of data. We must then determine how close the results have to be to, or how large the X 2 value can be and still accept the Ho, and at what point we should decide to reject the Ho. This is the probability or confidence level. We would expect that for valid hypotheses the discrepancy between observed and expected would be small. If the discrepancy is small enough, than we accept it. Statisticians usually use the 0.05 probability level to make this discrimination. At the 0.05 probability level, we would say that only 5% of the time would we see large

4 discrepancies between essentially identical observed and expected results. 95% of the time, the discrepancy is smaller. Thus at the 0.05 probability level, there is a 5% chance that we would discard a valid hypothesis. We thus choose the critical X 2 value from the table under the P = 0.05 column. For the case of 3 degrees of freedom, the X 2 value is 7,815. Thus in an experiment producing a X 2 value less than or equal to 7.815, we would conclude that the discrepancy is low enough to accept the Ho. Greater than 7.815, we would reject the Ho. It is possible to use other probability levels. For any degree of freedom, the critical X 2 value decreases with increasing probability. Why settle for 5% probability when we can have 95%? or 99%. If you observe a X 2 value at the 95% level, there is very little difference between observed and expected results. But if you accept X 2 values only at 95%, and there is actually more variability in the experiment than you would like to accept and you are likely to reject the Ho when you should accept it. At P = 95%, 95% of the time there will be as much or more discrepancy between observed and expected, yet the Ho should be accepted. By increasing the probability level, you increase the chance of discarding correct hypotheses. By decreasing the probability level, you increase the chance of accepting incorrect hypotheses. There is yet another way to look at a X 2 table. You could take the experimentally determined X 2 value and find the closest critical X 2 value in the table and then determine the closest probability or confidence level. Suppose, for example, that you caluculated a X 2 value of 2.53 at 3 degrees of freedom falls between and 4.642, and falls, therefore, between the 0.5 and 0.2 probability levels. You could conclude, then, that you would expect to see that much variation % of the time. Because 2.53 is less than 7.815, the critical X 2 value, this is an acceptable result. Table of Chi Square Values Degrees of P=.99 P=0.95 P=0.8 P=0.5 P=0.2 P=0.05 P=0.01 Freedom Familiarize yourself with the X 2 test by the following exercises: 1. Go back to tables 1-4 and complete the X 2 sections.

5 Table 1 Results Observed Expected Obs - Exp (Obs - Exp)2 Exp Heads Tails Totals X 2 = Table 2 Results Observed Expected Obs - Exp (Obs - Exp)2 Exp 2 Heads HH Heads + Tails HT 2 Tails TT Totals X 2 =

6 Table 3 Results Observed Expected Obs - Exp (Obs - Exp)2 Exp 3 Heads HHH 2 Heads + 1 Tail HHT 1 Head + 2 Tails HTT 3 Tails TTT Totals X 2 = Table 4 Results Observed Expected Obs - Exp (Obs - Exp)2 Exp 4 Heads HHHH 3 Heads + 1 Tail HHHT 2 Heads + 2 Tails HHTT 1 Head + 3 Tails HTTT 4 Tails TTTT Totals X 2 =

7 PROBLEMS 1. You have some trick coins that land heads 60% of the time and tails 40%. Use the binomal expansion to calculate the probabilities of HH, HT, and TT. If you flip 2 coins 175 times, what are the numbers of each? HH HT TT probability 175 times 230 times 2. A trick penny lands heads 35% of the time and a trick nickel lands heads 55% of the time. Use the binomial expansion to find the probabilities of the various combinations of heads and tails. What would be the numbers if you flipped them 275 times? 465 times? probability P N P N P N P N H H H T T H T H 275 times 465 times The remaining questions have to do with the frequencies of marbles in the following Jars Jar 1 Jar 2 Jar 3 Jar 4 80 blue 70 green 50 black 50 orange 20 red 30 yellow 50white 50 brown

8 3. Use the binomial expansion to calculate the probabilities and combinations by drawing from the jars as indicated: Jars combinations probabilities Jars combinations probabilities Jars 1, 2, 3 combinations probabilities 4. Calculate the probabilities of each event below: a. pulling 10 blue and 10 red from jar 1 b. pulling 25 green and 18 yellow from jar 2 c. pulling 6 black and 15 white from jar 3 d. pulling 10 orange and 10 brown from jar 4

9 5. You draw from jars 2 and times and get the results below. Use X 2 to determine whether or not this result is expected. Results Observed Expected Obs - Exp (Obs - Exp) 2 Exp green + orange 65 green + brown 75 yellow + orange 28 yellow + brown 32 Totals X 2 = 6. You draw from jars 1 and times and get the results below. Use X 2 to determine whether or not this result is expected. Results Observed Expected Obs - Exp (Obs - Exp) 2 Exp blue +green 230 red + yellow 38 blue + yellow 115 red + green 67 Totals X 2 =

10 7. You draw from jars 1 and times and get the results below. Use X 2 to determine whether or not this result is expected. Results Observed Expected Obs - Exp (Obs - Exp) 2 Exp blue + black 65 red + black 75 blue + white 28 red + white 32 Totals X 2 =

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