Gene Expression Analysis
104
Relative Quantity
By definition, relative quantity (
Δ
C(t)) data are not normalized. This method is used to
quantitate samples that do not include any reference genes (targets). Typically, researchers are
confident in one of the following considerations when they set up their experiment:
•
Each sample represents the same amount of template in each biological sample,
possibly the same mass of RNA or cDNA in each well
•
Any variance in the amount of biological sample loaded will be normalized after the
run by some method in the data analysis outside of the software. For example, a
researcher might choose to simply divide the relative quantity value by the
normalizing factor, possibly the mass of nucleic acid loaded for each sample, or the
number of cells from which the nucleic acid was isolated.
Select
Relative Quantity (
Δ
C(t))
from the pull-down menu in the chart controls of the Gene
Expression tab to run a Relative Quantity (
Δ
C(t)) analysis.
TIP: To compare results to data from other gene expression experiments, open a
new Gene Study (page 111), or add a data file to an existing Gene Study.
Adjusting Gene Expression Data
After selecting your analysis method, adjust the data you view in the Gene Expression tab by
changing the settings options to the right of the chart.
G
RAPH
D
ATA
Graph data options allow you to present the data in the graph with one of these two options:
•
Relative to control.
Graph the data with the axis scaled from 0 to 1. If you assign a
control in your experiment, select this option to quickly visualize upregulation and
downregulation of the target
•
Relative to zero.
Graph the data with the origin at zero
X-A
XIS
O
PTIONS
The X-axis option allows you to select the x-axis data of the Gene Expression graph:
•
Target.
Select this option to graph the target names on the x-axis
•
Sample.
Select this option to graph the sample names on the x-axis
Y-A
XIS
O
PTIONS
The Y-axis option allows you to show the Gene Expression graph in one of these three scales:
•
Linear.
Select this option to show a linear scale
•
Log 2.
Select this option to evaluate samples across a large dynamic range
•
Log 10.
Select this option to evaluate samples across a very large dynamic range
S
CALING
O
PTIONS
Select
Normalized Gene Expression (
ΔΔ
C(t))
to activate the scaling options in the Gene
Expression graph. Select one of these scaling options to calculate and present your data in a
manner that best suits your experimental design:
•
Unscaled expression.
This option presents the unscaled normalized gene expression
Summary of Contents for CFX384
Page 9: ...Table of Contents viii ...
Page 49: ...Protocols 40 ...
Page 89: ...Data Analysis Overview 80 ...
Page 149: ...Resources 140 ...
Page 157: ...Index 148 ...
