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ecs15
 

Lab2


This lab is divided into two parts:

- In part I, you will do online tutorials supplied by Microsoft to help you better understand how to use Excel workbooks, formulas, charts, etc..

- In part II, you will apply the knowledge you have just learned to analyze actual experimental data (biological data on gene expression).

Just like for Lab1, you will have to use Internet Explorer to run the tutorials.  If you have troubles starting the program, you may have to click the message bar of Internet Explorer to permit the download of the ActiveX program. 

The big difference however is that you will not have to save your work as you progress through the tutorials: your handout for this lab will be based solely on part II. I strongly advise however that you go through the tutorials, as it will help you through this part II.


Part I: Basics of Excel

You have three options, based on the version of Excel you will use: Excel2003, Excel2007, and Excel2010. If you are in the lab, I strongly advise that you go over the tutorials for Excel2010, as this is the version that is available on the computer labs.

- option 1: Excel 2003

Go to: http://office.microsoft.com/en-us/training/CR006183114.aspx which has a list of the Microsoft Excel 2003 Courses.

The tutorials you will be doing are:

  1. Audio course: Get to know Excel: Create your first workbook
  2. Get to know Excel: Enter formulas
  3. Charts I: How to create a chart

After each tutorial, to get back to the Excel 2003 training page you can either use the down arrow of your browser to get to the CR06… web page, or click “Return to Training on Microsoft Office Online”, and then select the Office 2003 tab in the Browse Training by Product area.

 

- option 2: Excel 2007

Go to: http://office.microsoft.com/en-us/training/CR010047968.aspx which has a list of the Microsoft Excel 2007 Courses.

The tutorials you will be doing are:

  1. Get to know Excel 2007: Create your first workbook
  2. Get to know Excel 2007: Enter formulas.
  3. Charts I: How to create a chart in Excel 2007

 After each tutorial, to get back to the Excel 2007 training page you can either use the down arrow of your browser to get to the CR01… web page, or click “Return to Training on Microsoft Office Online”, and then select the Office 2007 tab in the Browse Training by Product area.

 

- option 3: Excel 2010

Go to: http://office.microsoft.com/en-us/excel-help/CH010369467.aspx which has a list of the Microsoft Excel 2010 Courses.

The tutorials you will be doing are:

  1. Get to know Excel 2010: Create your first spreadsheet
  2. Get to know Excel 2010: Create formulas.
  3. How to create a basic chart in Excel 2010

 After each tutorial, to get back to the Excel 2007 training page you can either use the down arrow of your browser to get to the CR06… web page, or click “Return to Training on Microsoft Office Online”, and then select the Office 2007 tab in the Browse Training by Product area.

 

Part II: Analyzing Biological Data

 A simple experiment was designed to analyze the effects of noise on gene expression within a cell: a cell has been engineered to contain two genes (which we will label as C and Y) that are supposed to be expressed identically.  In the presence of noise however, the expression levels will differ. There are two possible source of noise:

- extrinsic noise: noise related to all external factors that may affect gene expression

- intrinsic noise: noise related to the gene expression machinery itself.

Two different experiments were conducted, each with a different type of cell. In experiment 1, data (i.e. expression levels for C and Y) were collected for 48 cells, while in experiment 2, data were available for 36 cells. The raw data are available in the file: Data_Lab2.xlsx

 Analyzing the data:

1) Download the data file Data_Lab2.xlsx

2) Some of the data are erroneous: these correspond to cases in which either C or Y is 0. Remove those rows from the file, for each experiment.

3) Generata a plot (scattered plot) of Y as a function of C for each experiment

4) Compute the levels of intrinsic, hint2, extrinsic, hext2, and total htot2 noise in each experiment. You will use the formula:

 Formula_Lab2.png

where <> stands for the average over all cells included in the experiment.

5) Generate a small report using Word that gives, for each experiment:

       - the plot of Y as a function of C. Make sure that:

                   - your plot has a title

                   - the ranges for values on the X-axis and Y-axis are the same

                   - you provide labels for the X and Y axis

                   - data points are shown as circles

       - the three noise values hint2, hext2, and htot2

 

Turn in your homework using Smartsite

It is very important to turn in your assignment. If you do not turn in, you will not get your credit. If you are not sure, ask a TA for help.

After submitting your report written using Word, you are done.  Don't forget to use the Start button to logout from the lab computers!

 

Grading

Please look at the table below to check the points for each part of the lab.

 Presentation of Word document: 4 points

  Plot Y=f(C) Three noise values
Experiment 1 7 points 6 points
Experiment 2 7 points 6 points

 

There is a total of 30 points for this assignment.

 
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