Bio-Rad Firmware & Software Updates - Manual (Page 121)

Gene Expression Analysis
110
• GOI = Gene of interest (target)
Normalized Expression Scaled to Average Expression Level
When the run does not include controls, scale the normalized expression (NE) for each target
(gene) by dividing the expression level of each sample by the geometric mean level of
expression of all the samples. The software sets the average level of expression to a value of 1
and rescales all the sample expression levels. The average scaling is calculated by this
formula:
Where:
• GOI = Gene of interest (target)
• GM = Geometric mean of normalized expression for all samples
Standard Deviation for the Scaled Normalized Expression
Re-scaling the scaled normalized expression (NE) value is accomplished by dividing the
standard deviation (SD) of the normalized expression by the normalized expression value for
the highest (MAX) or lowest (MIN) expression level, depending on which scaling option you
choose.
NOTE: When a control sample is assigned, you do not need to perform this
rescaling function on the standard deviation.
The formula for this calculation is shown here:
Where:
• NE = Normalized expression
• SD = Standard deviation
• GOI = Gene of interest (target)
• MAX = Highest expression level
• MIN = Lowest expression level
Regulation
Regulation is a measure of the increase or decrease in the expression of a target for an
experimental versus a control sample and is determined as follows:
Where:
• RNE = Relative normalized expression; this is the same as normalized expression
when a control is selected
Scaled Normalized Expression
sample (GOI)
Normalized Expression
sample (GOI)
Normalized Expression
GM (GOI)
---------------------------------------------------------------------------- =
SD Scaled NE
sample (GOI)
SD NE
sample (GOI)
NE
MAX or MIN (GOI)
--------------------------------------- =
For RNE 1 Regulation
 
RNE =
For RNE 1 Regulation
 
1 –
  RNE 
=