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And now, introducing
to these fine young
students of biology….
SPSS
for statistical
analysis of data
Statistics & Biology Lab
This semester is the continutation of a new initiative in our biology curriculum. This involves an integration of our Bio I: Cells Lab with the statistics course that most incoming biology students will be taking (Mat 1281). Data collected in Cells lab will be used for Mat 1281 examples, problems, and projects. Mat 1281 students will use their new statistical skills and will share what they have learned about our data as part of team presentations in Cells Lab. Even if you are not currently in Mat 1281, you will benefit from being part of our data analysis projects and can contribute in many ways to your own team’s presentation (coming later in November). Upperclassmen in our class bring in a wide range of experience. We are looking forward to the team presentations and discussion & ideas that they will stimulate.
This day’s session in the computer lab will introduce ALL Cells lab students to a statistical package they can use this semester and in the future for data analysis.
SPSS & SJU
Saint Joseph's University has purchased a network license for the statistical program SPSS for use on our computer network. This program is available for student use at the computer labs and computer classrooms on campus. Students who are currently taking MAT 1281 will purchase a student version of SPSS along with their statistics textbook and can install this on their own computers. Students in Mat 1281 will learn more about the types of statistical analyses and features of the programs in their math class. Cells lab teams can use this program later to analyze one of the data sets we will collect during Lab 1.
Introduction to SPSS
In today’s session you will be introduced to SPSS by:
Setting up the variables for a new data file Entering some sample data Having SPSS calculate some statistics and produce graphs from the data set Importing data from a text file
To begin…
- To begin, double-click on the SPSS icon or click on Start then Choose Programs and find the category for SPSS and choose the first option line for SPSS version 16.0 (or version you have)
- From the opening menu, select “ Type in Data ” and click on OK.
- Orient yourself to the program window: Notice the window that shows is called the Data Editor window (title in blue bar at top). It has two views, the Data View and the Variable View. Click between the two views by clicking on the “tabs” at the bottom of the window
You will use two major windows when working: the Data Editor window and the SPSS Viewer window. We will use the Data Editor window for defining variables and entering data. The SPSS Viewer will appear when you begin analyses of an established data file.
Defining Variables for Our Data Set
- The sample data set we will work with (full data shown later in Table I of this handout) is a set of measurements of cells from the meristematic region of onion and corn root tips.
These measurements were taken for each cell measured: length in ocular units – measured down the length of the root tip width in ocular units - measured across the root tip width
Thus, the length and width are two variables to define for our data set in the next step.
In the Variable View of the Data Editor : This view is used for defining variables and specifying their characteristics. Type length and width in the first two rows for Name “Name” s of variables must be short and not contain symbols like # or * or spaces.
Name Type Width Decimals Label Values 1 length 2 width
Automatically, default characteristics for the variable will show. We can then adjust these.
Entering Data
- In the Data View of the Data Editor : The Data View is used for entering data The columns are for each variable and each row indicates each case o variable = species, length, width o case = each cell measured in our data set Enter the data from Table I for the 18 cells measured o click in a box and type in the value, the data entry is very easy
Table I. Sample data for length (down length of root) and width (across root width) of cells in a similar region of two different root tip specimens. Values are shown in ocular units. Calibration of the microscope used established that actual size would be 2.33 um/ocular unit. Type of root* cell length cell width In ocular units in ocular units 1 1 10.5 7 2 1 12 8 3 1 11.5 9 4 1 8 4. 5 1 17 6 6 1 12 10 7 1 9 6 8 1 9 7 9 1 12 6 10 2 3 12 11 2 2 11 12 2 4 10 13 2 5 12 14 2 4.5 8. 15 2 2 9 16 2 4 17 17 2 4 8 18 2 3 10
Note: The corn data are listed correctly Length was defined by the measurer as the dimension of the cell up/down the column of cells, along the length of the root. These cells did indeed seem wider than they were “tall” in appearance.
*Abbeviations for type of root are 1 = onion (Allium) and 2 = corn ( Zea mays ).
8. A note about the species column: The value labels button (3nd^ to end on toolbar, looks like a price tag) can be used to see onion or corn instead of the entered 1 or 2, since we labeled these values.
Proof-read & Save your file
- After entering data always do two things: 1. PROOF the entries against the original data set!! 2. SAVE your file_. To do this click on File Save. In the computer lab or_ library, save only to your J: drive (shows your login name on the list of drives or says “homes”) or to a USB drive or CD. After your initial save, resave periodically by clicking on the small diskette icon.
Transforming to actual size in micrometers
10. The values were given as measured width and length in ocular units. However, we will be interested in the actual width and length in micrometers. These can indeed be new variables for our data set. However, we already used the names “length” and “width”. No problem, we’ll change the measured length and width to mlength and mwidth and use length and width for the calculated actual dimensions.
In the Variable View of the Data Editor : click on the cell for the Name length. Double-click at the start of length (before the l), the cursor will appear Add an m so you will now call this mlength for measured length in ocular units. Also rename the width as mwidth
Name Type Width Decimals Label Values 1 species Numeric 8 0 type of root tip {1,onio 2 mlength Numeric 8 1 Measured length in ocular units None 3 mwidth Numeric 8 1 Measured width in ocular units None
11. Now, we’ll have SPSS calculate the actual length and width and update our data table: Click on Transform and choose Compute Variable from the pull-down menus across the top. In target variable box enter length Click on the Type & Label button just below your entry The variable’s label can be typed in as actual length in micrometers Numeric type (already selected) is okay for this new variable. Click Continue.
The formula for actual length would be mlength x 2.33. In the compute variable window:
Find mlength in the list of variables, click to select. Click the arrow key to import this over to the Numeric Expression box Use the mouse to click on the onscreen keypad to put in the x 2.33 ( _use the mouse to click on the onscreen keypad to enter the
- and 2.33, NOT on computer keyboard keys_ ) Click on OK.
Then, do the same for width = mwidth x 2. in Type & Label you can label this new variable actual width in micrometers
In the Data View of the Data Editor :
- Notice that the actual size columns have been filled in with the transformed values!
Examples of output of with split file ON
= split file button
FREQUENCIES
Analyze Descriptive Statistics
Frequencies
- Split file: compare by group
- Use Statistics to pick which stats when in Frequencies window
- Additional variables go in columns
- If split file with organize output by groups, you get separate tables.
DESCRIPTIVES
Analyze Descriptive Statistics Descriptives
- Split file: compare by group
- Additional variables will go on rows
- Use options to choose which stats when in Descriptives window
- If split file with organize output by groups, you get separate tables for onion and corn
Descriptive Statistics type of root N Minimum Maximum Mean Std. Deviation onion actual width in micrometers 9 10.48 23.30 16.4394 3. Valid N (listwise) 9 corn actual width in micrometers 9 18.64 39.61 25.2417 6. Valid N (listwise) 9
Examples of output of with split file OFF
= split file button (choose analyze all cases)
EXPLORE
Analyze Descriptive Statistics Explore
- Send your grouping variable (independent) such as Species into “Factor List” in Explore Window
- If more than one dependent variable (length, width), each will in go in panels below one another
- This is only part of the output. Also will give charts.
- Good for an initial exploration of the data set. Lots of output in a few clicks.
MEANS
Analyze Compare Means Means
- send grouping variable into Independent List box
- Multiple dependent variables shown in columns (length, width,…)
- Use Options button to go to window to change which stats – also has
median, max, min, etc.
Examining Some Graphs of the Data Set’s Statistics
- There are a number of different types of graphs used in the statistical examination of data. The new version of SPSS has a “ Chart Builder ” for drag and drop set up of charts and graphs. If you’ve used SPSS before and prefer those menus, you can go through Legacy Dialogs to see dialog boxes used in earlier versions. We’ll try a box plot comparing the data by species again.
If you use Graph Legacy Dialogs , these are the steps: choose BoxPlot. Click on Define (leave “Simple” button selected) Move the actual length in micrometers to the Variable spot by selecting & clicking arrow Move the type of root to the Category Axis spot by selecting & clicking arrow Click OK
Click on Graphs from the top pull-down menus Choose Chart Builder o The program reminds you at this point to make sure your grouping variables are defined correctly. This means that you have set the “measure” column to nominal or ordinal. The icon next to the variable will show you its measure status. If you see the balls or bars (not ruler) for your grouping variable, you are okay. Click OK. If not, you can fix via the menus offered or cancel the Chart Builder and go back to Variable View of the Data Editor window and fix.
From the Gallery below, choose Boxplot and choose the first type by dragging the picture up & dropping into preview box (dark arrow, “do 1 st”).
Drag the dependent variable to Y axis (measured value such as width or length) and independent variable to the X axis (grouping variable, such as species) shown as thin arrows (“do 2 nd^ ”).
Click on OK. The graph should show up in your Output file.
Scroll down to see the graph. The dark line shows the median value (middle value) and the red boxes encompass half of the values (25% on either side of median). The bars will show the max and min and “outliers” are circles. The two root data sets don’t even overlap (min onion > max corn), this is quite interesting... Mat 1281 students will learn a lot more on how to use these plots. But, now you know they are very easy to generate in SPSS!
- The last graph we will try is a histogram , a very common graph for looking at a population. But, since the onion and corn are so different, perhaps you would want to do them separately. The Chart Builder allows us to panel the graphs to show the two species in separate panels.
In Graphs Chart Builder In Gallery, find Histogram Drag & Drop the 1st^ type into the preview window (thick arrow). Drag & Drop the actual length in micrometers onto the X axis (thin arrow). In the histogram, the Y axis will be the frequency or count by default, so you do not specify any Y axis variable.
Before clicking OK, click on the tab for Groups/Point ID Check Rows Panel (if you want them side by side, use columns panel variable) Drag & Drop your grouping variable (species) into the Panel? Box Your Chart Preview should look like this: (note, this doesn’t show your actual data)
Click OK. The actual chart will show up in your output file.
- PRINT YOUR BOXPLOT OR HISTOGRAM to turn in for this assignment. Make sure you insert your name somewhere in the output file so that it is easily identified as your own. One way is: Double-click on the graph in the output file to call up Chart editor Choose Options, Text box. Then type your text (name or other personalized text). Click back on Output file in some other area to close Chart editor Make sure graph is selected (click on it so there is a solid box outline around) and print. Duplicates of output from friends or teammates will not be accepted. It must be your own, so personalize it.
- Re-save your data file in the Data Editor window. If you want to keep your output file of the histograms, etc to look at later, Save this in the SPSS Viewer window. It is a separate file.
