Microsoft Word - big assignment 13 instructions.docx

Big Assignment 13 aka pre-test for lab exam 2 Instructions

1. you are studying Snurfles (link to webpage)

which follow a classic Mendelian autosomal

dominant inheritance pattern for the following

two traits- Fur color and Fins:

In your

eeding experiments you perform a

dihy

id cross for Fur Color and Fins

It turns out that Snurfles are rather fecund, and in a short

span of time you have 200 offspring for which you have

tallied phenotypes as follows:

Phenotype Obs

Exp

prop*

Yellow, Finless XXXXXXXXXX

Green, Finned XXXXXXXXXX

Yellow, Finned XXXXXXXXXX

Green, Finless XXXXXXXXXX

*the expected proportions are from the Punnett square which gives a phenotype ratio of 9:3:3:1

Use the data on the “Snurfle” tab of the Excel Spreadsheet, or 01snurfle.csv, to complete the prompts

on the answer form.

2 You are investigating a new drug that might lower anxiety. The drug was shown to be safe in

humans, so now for some efficacy testing:

Twenty participants with clinical anxiety disorder are randomly assigned to one of four treatment

groups, in which they receive the listed treatment for 3 weeks. At the end of the trial, the participants

took an anxiety test. The scores, co

ected for initial anxiety score, are reported in the table below.

(Lower scores indicate lower anxiety levels.)

Control

Placebo

no Drug

Low

Dose

Moderate

Dose

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Analyze the data* to determine if there is any difference in anxiety scores between the groups, and if

there is a difference, determine and explain which treatment is most effective: record your responses

to the prompts on the Answer Sheet.

*Data is also available on the Excel Spreadsheet under the “Anxiety” tab, and the 02Anxiety.csv file.

3. The oceanic field cricket, Teleogryllus oceanicus are

invasive species on the Hawaiian archipelago. They

have an interesting relationship with an endemic fly

Ormea ochracea which serves as a wonderful

example of natural selection.. The male field crickets

chirp to attract their mates, however the chirping also

attracts the parasitoid fly, which would thus attack and

ultimately kill chirping males. This has led to a

dramatic shift in the chirping behavior of the crickets

esulting in, among other things, silent nights with no cricket

chirping on some of the Islands. You are on an island with

crickets that still chirp and are interested if abiotic differences

etween the islands such as temperature are inhibiting the

parasitism of crickets by the fly in some way. Determine if

there is a trend between the air temperature and the amount of

crickets chirps you hear to help find out how these cricket

populations are chirping without going extinct.

You collect the following set of data for chirp rates and temperatures throughout the island:

Temperature Chirp Rate

C Hz

31.4 20

22.0 16

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

26.4 15

XXXXXXXXXX

27.0 16

28.6 17

XXXXXXXXXX

Which is also available on the Excel sheet and as 03Crickets.csv

4. Crop rotation is a common strategy used to improve the

yields of certain crops in subsequent growing seasons. An

experiment was performed to assess the effects of crop

otation plant type and crop rotation plant density levels on

the yield of corn, the primary crop of interest. A field was

separated into 12 plots and each of the treatments was

andomly applied. After 2 months of growth of the rotated

crops, the plots were cleared and corn seeds were applied

evenly to each plot. After 5 months of growth of the corn,

the yields were assessed. The data, in kg/m2, are shown

elow, and is available on the Crop tab of the Excel

Spreadsheet, and the csv file 04Crops:

planting density

Rotation

Variety low medium high super

Pea XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX3

Soy XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Wheat XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Determine if crop rotation plant type, crop rotation density, or a combination of both have any effect

on the yields of corn in this field. What treatment should the farmers use to maximize the yield?

Record responses on the answer form…

5. In preparation for replicating an

experiment involving rats and beer, you

would like to use rats already on hand to

save costs, but they are of different colors,

and you are concerned that for rats natural

life span and color might not be

independent traits. To verify this, you

consult some old logs listing rat color and

life span, and assemble the following data

table:

And the data is also available on the Spreadsheet

“05Rats” tab, as well as 05Rats.csv

Complete the prompts on the answer form…

6. Read the linked paper;

L M Klevay, R J Moore, Beer mitigates some effects of copper deficiency in rats, The American Journal of

Clinical Nutrition, Volume 51, Issue 5, May 1990, Pages 869–872, https:

doi.org/10.1093/ajcn/ XXXXXXXXXX

And respond to the prompts about it on the answer form.

Then, consult the data on the Beer tab of the excel sheet

What can you conclude from that (spreadsheet) data?

Record your analysis on the answer form.

lifespan

short medium long

own XXXXXXXXXX

white XXXXXXXXXX

grey XXXXXXXXXX

BONUS:

Create a data set and back-story for a real or fictitious biological study subject that serves as a model

for one of the following statistical tests:

Chi-Square

! Goodness of Fit

! Independence

! HOV

One Factor ANOVA

! Data with HOV

! Data that needs to be transformed

! Two Factor ANOVA

! Regression

! Co

elation

Create a data set that can be used in an exercise like, well, this one, or maybe an exam.

On the Answer form…

Exercise 13: Unit 2 summary Answers Name

Here are some symbols to copy and paste maybe: α β μ σ ν χ2 λ ρ Σ

1. For the Snurfles Punnett Square Dihy

id Cross:

A. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).

B. What type of data are you working with? i.e. measurements, counts, ratios, discreet or continuous, etc. (replace this text with your answer).

C. if you have probabilities or proportions, are they extrinsic to the data, or intrinsic, i.e. do you have to calculate them from the data or are they a ‘given’? (replace this text with your answer).

D. Which Statistical Test will you perform? i.e. χ2 GOF/Independence/HOV, One Factor ANOVA, Two Factor ANOVA, Co

elation, Regression, student’s t-Test, etc. (replace this text with your answer).

E. Conducting the Test:

Include a plot if appropriate

State the Null and Alternative Hypothesis, if appropriate

Results of pre-test, if appropriate (just test and p-value or calc vs. crit)

Copy and paste tables if appropriate

G. Results of the Test:

Test statistics, calc vs crit, p-values as appropriate.

Post-hoc tests results, if appropriate.

Include tables if appropriate.

Include Plots if appropriate.

H. Conclusion:

What is your interpretation of the results of the tests? Provide detail! If you reject or fail to reject any null hypothesis, what does this mean in terms of the scientific question you are trying to answer? What does it mean if the observed data does or does not match the predicted?

In this case, the assumption in the Dihy

id cross is that the expected probabilities only hold true if there is a strict Dominance pattern (not co- nor incomplete), and that the two traits assort independently and segregate randomly. If the actual offspring counts do not match the expected, what does this tell us is happening (or not happening) with these traits in Snurfles?

2. For the Efficacy Study on the Anti Anxiety Drug

A. What Scientific Question are you answering with your study?

B. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).

C. if you have probabilities or proportions

Big Assignment 13 aka pre-test for lab exam 2 Instructions

1. you are studying Snurfles (link to webpage)

which follow a classic Mendelian autosomal

dominant inheritance pattern for the following

two traits- Fur color and Fins:

In your

eeding experiments you perform a

dihy

id cross for Fur Color and Fins

It turns out that Snurfles are rather fecund, and in a short

span of time you have 200 offspring for which you have

tallied phenotypes as follows:

Phenotype Obs

Exp

prop*

Yellow, Finless XXXXXXXXXX

Green, Finned XXXXXXXXXX

Yellow, Finned XXXXXXXXXX

Green, Finless XXXXXXXXXX

*the expected proportions are from the Punnett square which gives a phenotype ratio of 9:3:3:1

Use the data on the “Snurfle” tab of the Excel Spreadsheet, or 01snurfle.csv, to complete the prompts

on the answer form.

2 You are investigating a new drug that might lower anxiety. The drug was shown to be safe in

humans, so now for some efficacy testing:

Twenty participants with clinical anxiety disorder are randomly assigned to one of four treatment

groups, in which they receive the listed treatment for 3 weeks. At the end of the trial, the participants

took an anxiety test. The scores, co

ected for initial anxiety score, are reported in the table below.

(Lower scores indicate lower anxiety levels.)

Control

Placebo

no Drug

Low

Dose

Moderate

Dose

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Analyze the data* to determine if there is any difference in anxiety scores between the groups, and if

there is a difference, determine and explain which treatment is most effective: record your responses

to the prompts on the Answer Sheet.

*Data is also available on the Excel Spreadsheet under the “Anxiety” tab, and the 02Anxiety.csv file.

3. The oceanic field cricket, Teleogryllus oceanicus are

invasive species on the Hawaiian archipelago. They

have an interesting relationship with an endemic fly

Ormea ochracea which serves as a wonderful

example of natural selection.. The male field crickets

chirp to attract their mates, however the chirping also

attracts the parasitoid fly, which would thus attack and

ultimately kill chirping males. This has led to a

dramatic shift in the chirping behavior of the crickets

esulting in, among other things, silent nights with no cricket

chirping on some of the Islands. You are on an island with

crickets that still chirp and are interested if abiotic differences

etween the islands such as temperature are inhibiting the

parasitism of crickets by the fly in some way. Determine if

there is a trend between the air temperature and the amount of

crickets chirps you hear to help find out how these cricket

populations are chirping without going extinct.

You collect the following set of data for chirp rates and temperatures throughout the island:

Temperature Chirp Rate

C Hz

31.4 20

22.0 16

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

26.4 15

XXXXXXXXXX

27.0 16

28.6 17

XXXXXXXXXX

Which is also available on the Excel sheet and as 03Crickets.csv

4. Crop rotation is a common strategy used to improve the

yields of certain crops in subsequent growing seasons. An

experiment was performed to assess the effects of crop

otation plant type and crop rotation plant density levels on

the yield of corn, the primary crop of interest. A field was

separated into 12 plots and each of the treatments was

andomly applied. After 2 months of growth of the rotated

crops, the plots were cleared and corn seeds were applied

evenly to each plot. After 5 months of growth of the corn,

the yields were assessed. The data, in kg/m2, are shown

elow, and is available on the Crop tab of the Excel

Spreadsheet, and the csv file 04Crops:

planting density

Rotation

Variety low medium high super

Pea XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX3

Soy XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Wheat XXXXXXXXXX

XXXXXXXXXX

XXXXXXXXXX

Determine if crop rotation plant type, crop rotation density, or a combination of both have any effect

on the yields of corn in this field. What treatment should the farmers use to maximize the yield?

Record responses on the answer form…

5. In preparation for replicating an

experiment involving rats and beer, you

would like to use rats already on hand to

save costs, but they are of different colors,

and you are concerned that for rats natural

life span and color might not be

independent traits. To verify this, you

consult some old logs listing rat color and

life span, and assemble the following data

table:

And the data is also available on the Spreadsheet

“05Rats” tab, as well as 05Rats.csv

Complete the prompts on the answer form…

6. Read the linked paper;

L M Klevay, R J Moore, Beer mitigates some effects of copper deficiency in rats, The American Journal of

Clinical Nutrition, Volume 51, Issue 5, May 1990, Pages 869–872, https:

doi.org/10.1093/ajcn/ XXXXXXXXXX

And respond to the prompts about it on the answer form.

Then, consult the data on the Beer tab of the excel sheet

What can you conclude from that (spreadsheet) data?

Record your analysis on the answer form.

lifespan

short medium long

own XXXXXXXXXX

white XXXXXXXXXX

grey XXXXXXXXXX

BONUS:

Create a data set and back-story for a real or fictitious biological study subject that serves as a model

for one of the following statistical tests:

Chi-Square

! Goodness of Fit

! Independence

! HOV

One Factor ANOVA

! Data with HOV

! Data that needs to be transformed

! Two Factor ANOVA

! Regression

! Co

elation

Create a data set that can be used in an exercise like, well, this one, or maybe an exam.

On the Answer form…

Exercise 13: Unit 2 summary Answers Name

Here are some symbols to copy and paste maybe: α β μ σ ν χ2 λ ρ Σ

1. For the Snurfles Punnett Square Dihy

id Cross:

A. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).

B. What type of data are you working with? i.e. measurements, counts, ratios, discreet or continuous, etc. (replace this text with your answer).

C. if you have probabilities or proportions, are they extrinsic to the data, or intrinsic, i.e. do you have to calculate them from the data or are they a ‘given’? (replace this text with your answer).

D. Which Statistical Test will you perform? i.e. χ2 GOF/Independence/HOV, One Factor ANOVA, Two Factor ANOVA, Co

elation, Regression, student’s t-Test, etc. (replace this text with your answer).

E. Conducting the Test:

Include a plot if appropriate

State the Null and Alternative Hypothesis, if appropriate

Results of pre-test, if appropriate (just test and p-value or calc vs. crit)

Copy and paste tables if appropriate

G. Results of the Test:

Test statistics, calc vs crit, p-values as appropriate.

Post-hoc tests results, if appropriate.

Include tables if appropriate.

Include Plots if appropriate.

H. Conclusion:

What is your interpretation of the results of the tests? Provide detail! If you reject or fail to reject any null hypothesis, what does this mean in terms of the scientific question you are trying to answer? What does it mean if the observed data does or does not match the predicted?

In this case, the assumption in the Dihy

id cross is that the expected probabilities only hold true if there is a strict Dominance pattern (not co- nor incomplete), and that the two traits assort independently and segregate randomly. If the actual offspring counts do not match the expected, what does this tell us is happening (or not happening) with these traits in Snurfles?

2. For the Efficacy Study on the Anti Anxiety Drug

A. What Scientific Question are you answering with your study?

B. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).

C. if you have probabilities or proportions

Answered Same DayNov 30, 2021

01 Snurfles

Snurfle Traits from Paper snurfle data, sorted with calculations

Phenotype Obs Exp prop* Yellow, No Fins Yellow,Fins Green, No Fins Green, Fins SUM

Yellow, Finless 84 0.5625 observed # 84 54 40 22 200

Green, Finned 22 0.1875 expected # 112.5 37.5 12.5 37.5 200

Yellow, Finned 54 0.1875 contribution 7.22 7.26 60.5 6.4066666667 81.3866666667

Green, Finless 40 0.0625

200 1

Test Stats

calc= 81.3867

df= 3 g= 4 r= 1

α= 0.05

crit= 7.818

p-value= 1.547x10^(-17)

*from Mendelian Genetics Dihy

id cross

Since p < 0.05 reject H0

The phenotypes are not distributed as per expected proportion.

Sheet4

Anova: Single Facto

SUMMARY

Groups Count Sum Average Variance

Control 5 171 34.2 23.2

Placebo 5 144 28.8 31.7

Low Dose 5 108 21.6 42.8

Moderate Dose 5 47 9.4 25.8

ANOVA

Source of Variation SS df MS F P-value F crit

Between Groups 1725 3 575 18.6234817814 0.0000180377 3.2388715224

Within Groups 494 16 30.875

Total 2219 19

02 Anxiety

Adjusted Anxiety Score

Control Placebo Low Dose Moderate Dose

32 35 18 16

40 28 13 10

38 34 27 3

28 22 21 12

33 25 29 6

Sheet1

SUMMARY OUTPUT

Regression Statistics

Multiple R 0.8351437868

R Square 0.6974651446

Adjusted R Square 0.6741932326

Standard E

or 0.9715177252

Observations 15

ANOVA

df SS MS F Significance F

Regression 1 28.287326358 28.287326358 29.9702553871 0.0001066719

Residual 13 12.2700069754 0.9438466904

Total 14 40.5573333333

Coefficients Standard E

or t Stat P-value Lower 95% Upper 95% Lower 95.0% Upper 95.0%

Intercept 6.4724558986 1.8765289643 3.4491638667 0.0043150396 2.418461549 10.5264502481 2.418461549 10.5264502481

C 0.3814650163 0.0696802169 5.4745096024 0.0001066719 0.2309300601 0.5319999725 0.2309300601 0.5319999725

03 Crickets

Temperature Chirp Rate

C Hz

31.4 20

22.0 16

34.1 19.8

29.1 18.4

27.0 17.1

24.0 15.5

20.9 14.7

27.8 17.1

20.8 15.4

28.5 16.2

26.4 15

28.1 17.2

27.0 16

28.6 17

24.6 14.4

Hz 31.444444444444439 21.999999999999996 34.05555555555555 29.055555555555554 26.999999999999996 24 20.944444444444446 27.777777777777779 20.777777777777782 28.499999999999996 26.444444444444439 28.111111111111107 26.999999999999996 28.611111111111111 24.611111111111107 20 16 19.8 18.399999999999999 17.100000000000001 15.5 14.7 17.100000000000001 15.4 16.2 15 17.2 16 17 14.4

Sheet2

Anova: Two-Factor With...

Snurfle Traits from Paper snurfle data, sorted with calculations

Phenotype Obs Exp prop* Yellow, No Fins Yellow,Fins Green, No Fins Green, Fins SUM

Yellow, Finless 84 0.5625 observed # 84 54 40 22 200

Green, Finned 22 0.1875 expected # 112.5 37.5 12.5 37.5 200

Yellow, Finned 54 0.1875 contribution 7.22 7.26 60.5 6.4066666667 81.3866666667

Green, Finless 40 0.0625

200 1

Test Stats

calc= 81.3867

df= 3 g= 4 r= 1

α= 0.05

crit= 7.818

p-value= 1.547x10^(-17)

*from Mendelian Genetics Dihy

id cross

Since p < 0.05 reject H0

The phenotypes are not distributed as per expected proportion.

Sheet4

Anova: Single Facto

SUMMARY

Groups Count Sum Average Variance

Control 5 171 34.2 23.2

Placebo 5 144 28.8 31.7

Low Dose 5 108 21.6 42.8

Moderate Dose 5 47 9.4 25.8

ANOVA

Source of Variation SS df MS F P-value F crit

Between Groups 1725 3 575 18.6234817814 0.0000180377 3.2388715224

Within Groups 494 16 30.875

Total 2219 19

02 Anxiety

Adjusted Anxiety Score

Control Placebo Low Dose Moderate Dose

32 35 18 16

40 28 13 10

38 34 27 3

28 22 21 12

33 25 29 6

Sheet1

SUMMARY OUTPUT

Regression Statistics

Multiple R 0.8351437868

R Square 0.6974651446

Adjusted R Square 0.6741932326

Standard E

or 0.9715177252

Observations 15

ANOVA

df SS MS F Significance F

Regression 1 28.287326358 28.287326358 29.9702553871 0.0001066719

Residual 13 12.2700069754 0.9438466904

Total 14 40.5573333333

Coefficients Standard E

or t Stat P-value Lower 95% Upper 95% Lower 95.0% Upper 95.0%

Intercept 6.4724558986 1.8765289643 3.4491638667 0.0043150396 2.418461549 10.5264502481 2.418461549 10.5264502481

C 0.3814650163 0.0696802169 5.4745096024 0.0001066719 0.2309300601 0.5319999725 0.2309300601 0.5319999725

03 Crickets

Temperature Chirp Rate

C Hz

31.4 20

22.0 16

34.1 19.8

29.1 18.4

27.0 17.1

24.0 15.5

20.9 14.7

27.8 17.1

20.8 15.4

28.5 16.2

26.4 15

28.1 17.2

27.0 16

28.6 17

24.6 14.4

Hz 31.444444444444439 21.999999999999996 34.05555555555555 29.055555555555554 26.999999999999996 24 20.944444444444446 27.777777777777779 20.777777777777782 28.499999999999996 26.444444444444439 28.111111111111107 26.999999999999996 28.611111111111111 24.611111111111107 20 16 19.8 18.399999999999999 17.100000000000001 15.5 14.7 17.100000000000001 15.4 16.2 15 17.2 16 17 14.4

Sheet2

Anova: Two-Factor With...

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