BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
Lab 11
Analysis of Plant Partnerships data
Today we will analyze your data from the Plant Partnerships experiment that you designed and
executed over the last few weeks.
Discuss these questions in your groups and upload your data onto Moodle
Why did we do this experiment?
What traits can you measure?
What questions to you want to ask about your data?
What are your hypothesized answers to those questions?
STEPS IN THE DATA ANALYSIS
 Add today’s germination data into your Excel spreadsheet
 Make a new column for germination over all weeks (Y/N)
 Make a new column for morality over all weeks (A/D “alive” or “dead”)
 There can only be numbers or text in each column
 If there is no data (i.e. plant never germinated), leave the cell empty. Do not fill with a
zero or any other symbol
 Column headers should not have any symbols or spaces as shown below:
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Save as an Excel spreadsheet
Save again as “Text (tab delimited)”
Click “OK” to save the active sheet
Click “yes” to save without additional features
Don’t save again – just close the file
Open the statistical software JMP
BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
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Under “file menu” select “import” and “text others
Click on “options” and select labels from the top row
Click “open”
Check each column to make sure it indicates the right kind of data in indicated in the
check box
C = continuous (i.e. numerical where the number has meaning)
O = ordinal (i.e. order categories such as “small” “medium” and “large)
N = nominal (i.e. categories with no order such as Germinate “yes” or “no”)
You can change this in two ways
1. a drop down menu in the box
2. drop down menu called “column information”
If you have more than one species, analyze one at a time by highlighting all the rows you
don’t want to analyze and select “include/exclude” from the “rows” drop-down menu
All rows that are eliminated should now be marked with a symbol “.”
FOR ANALYSES OF CATEGORICAL DATA (data designated as “nominal”)
 From the “analyze” drop down menu, select “Fit X to Y” which will allow you to do a
contingency test
 Y” is the response variable, in this case “Germ” or “Mort”. Add this column header into
the appropriate box
 “X” is the factor that we altered experimentally, for example “Fungus” or “CFRhiz.” Add
the treatment column into the appropriate box.
 Click “run model”
 You will see a bar graph of the data, followed by a contingency table, and analyses.
FOR ANALYSES OF CONTINUOUS DATA (Numerical data – height, leaf number, etc.)
 From the “analyze” drop down menu, select “fit model” which will allow you to do an
“Analysis of Variance” which tests whether at least one of the treatment means differs
from the others
 “Y” is the response variable, in this case % survival. Add this column header into the
appropriate box
 “X” is the factor that we altered experimentally “Effects in the model”. Add the
treatment column into the appropriate box.
 Click “run model”
 To find out if at least one of the means is statistically different that the others, look for
“Prob>F” on your output. This is the p-value.
 To determine which means are significantly different from the others, you need to do
“post-hoc contrasts”
 Click on the side arrow by “Treatment” and select “Add contrast”
 To test whether there is a significant difference between two treatment means (or
between a treatment and a control), click “+” square to right of one of the treatments and
then click on the “-“ square to the right of the treatment you want to compare it to.
 Click “done” and look for the p-value, “Prob>F”
BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
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Do the next contrast by clicking for a second time on the side arrow near “treatment” and
selecting ‘contrast”
Write down every contrast you think you should do. Do them. And then write the pvalue associated that test (Make a table).
When you are you are done, save your file by going to the “edit” drop down menu and
selecting “journal.”
Save this file to the desk top. You will be able to open it in MS Word file to get the
ANOVA table and estimated means. You can cut and paste your ANOVA table directly
from the JMP output into you lab report or make one from scratch. Also, make a table in
your lab report that shows the p-values from each of the contrasts that you performed.
Steps for making a bar chart in Excel
1. Enter data into three columns from JMP ANOVA output
Treatment
Least Squares Means
Standard Error
2. Multiply the standard errors by 2
3. Make a bar chart of the data
Highlight Treatment column and the Least Squares means column you want to graph
The data range should appear automatically - click "next"
Click on the Chart Icon, click "yes"
Label your chart and the X and Y axes, then click "next"
4. Add error bars
Double click on the bars to get to the "Format Data Series" menu
Select Y- error bars both above and below the mean
Select "custom" and highlight the specific cells in the" 2*SE (Standard errors *2)" column
Do this for both "plus" and "minus"
WRITING LAB140
REPORTS
Sample Data Set up
120
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you should follow when you write
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FORMAT
Your report must be typed, spell-checked, double spaced, and have approximately 3-5 pages
long. Tables and Figures can be imbedded in the text or included as separate pages at the end
of the lab report. Late lab reports will not be accepted.
1. Title
2. Introduction
3. Materials and methods
4. Results
5. Discussion
BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
TITLE
The title should be interesting, concise, and reflect the content of the paper.
INTRODUCTION
The introduction should provide the reader with a context for understanding why
the research was conducted and why it is important. The research question and the
objectives for the study should be clearly stated in this section. In addition, you
should review at least one other paper from the primary literature that researched a
similar question. Any general information you provide should be cited. For this
purpose, it is okay to cite text books, other books, web pages etc. But there should
be at least one entry from the primary literature that is cited in this section and
appears in the bibliography. At the end of this section, you should explicitly state
the hypotheses you are testing.
MATERIALS AND METHODS
This section should outline the exact procedures that were followed in sentence and
paragraph form. Bulleted sentences are not acceptable. This should not be written like a
protocol but include sufficient detail such that another researcher could replicate the
experiment. (Soil, how the seed was prepped, the germination conditions, pot size,
planting date, measurement date …)
RESULTS
The results section should summarize the data from the experiments without discussing
their implications. You should ake a two tablese that presents the statistical results of
your study (ANOVA table and Contrasts from lab handout) and one figure (graphs) that
present the data visually. Each table and figure should have a sentence or two (figure or
table legend) that explains what is being shown. All columns and rows in tables and axes
in graphs should be labeled. Figures and tables should be numbered separately. The
narrative of the results section should discuss each result as shown in the table and each
result as presented in the figures. During the narrative, the author should refer to the
tables and figures by number. For example:
There was a statistically significant difference in final leaf number between plants
that were inoculated and those that were not (Table 1). Leaves of plants grown
with the inoculum were 46 % larger than those that were not (Figure 1).
DISCUSSION
In this section, the author should discuss whether or not the data supports their
hypothesis. Does the data contradict some prevailing notion or add another piece of
information to an already well understood question? You should compare your results
with those of the one primary literature source that you have found. The discussion is a
good place to describe any limitations of the study and suggest future experiments that
might more fully answer the question being asked.
BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
LITERATURE CITED
Please follow the examples given below for citing literature in your report.
When citing references in the body of the paper refer to articles by the author’s last name
and the date the paper was published. For example: “Douglas (2004) examined the
effectiveness of seven commonly used botanical preservatives in preventing microbial
growth” or “Seven commonly used botanical preservatives were found to be effective in
preventing microbial growth (Douglas, 2004).” When citing papers that have two
authors, both names must be listed. When three or more authors are involved, the Latin et
al. (et alia) meaning "and others" may be used. For example, a paper by Etterson,
Andrews and Rachinsky would be cited in the text as: “Etterson et al. (2003) have shown
that... “
Journal articles
Douglas, F.A. 2004. Use of botanicals as biopreservatives in foods. Food
Technology 58:20-28.
Books
Belk, C.M. and V.M. Borden. 2003. Biology: Science for Life. Prentice Hall
Publishers, Inc.
Web pages
Intergovernmental Panel on Climate Change. 2007. The AR4 Synthesis Report.
Retrieved February 2, 2009, from http://www.ipcc.ch/.
PLAGIARISM
Plagiarism is using another person’s ideas or words without clearly acknowledging the
source of that information. To avoid plagiarism be sure to provide a citation whenever
you use another person’s idea, opinion, or theory. You must also cite any facts, statistics,
graphs, etc that are not common knowledge. Obviously, using the exact same words as
someone else or turning in someone else’s work under your name qualifies as plagiarism.
It is very easy to run a few sentences from a paper through a software program to see
whether this particular report has been turned in before. In addition to failing to practice
an important skill, student’s who turn in the work of others risk of being expelled from
the University. See the UMD plagiarism policy by linking to:
BIOL 3601: PLANT DIVERSITY
DR. JULIE R. ETTERSON
SPRING 2009
LAB REPORT GRADING:
The following is the evaluation criteria that we will use to grade your lab reports.
I. Title
GRADING CRITERIA
Not excessively wordy
Contains descriptive words
POINTS
1
II. Introduction
Uses background from the primary literature
Identifies purpose of study
Explains significance of study
States hypotheses clearly
13
III. Materials and
Methods
Contains organized, precise information that would allow
study to be repeated
Identifies data that was collected
10
IV. Results
Presence of tables (two tables: ANOVA and Contrasts)
One bar graph
Complete description of tables and graphs in text
10
V. Discussion
Summary of purpose
13
States conclusions that are consistent with data
Explains unexpected results
Compares results to at least one other study from the primary literature
Describes limitations of the study and suggests future work
Emphasizes importance of study
VI. Literature Cited
Formatted correctly
Referenced appropriately in the text
VII. Style, Grammar, Spelling
Maintain a common tense throughout the paper
2
1
TOTAL POINTS = 50