Bio-Rad Firmware & Software Updates - Manual (Page 143)

Gene Expression Analysis
130
Normalized Expression Scaled to Lowest 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 lowest level of expression in all
the samples. The software sets the lowest level of expression to a value of 1 and rescales all
the sample expression levels. The lowest scaling is calculated by this formula:
Where:
• 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
Rescaling 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
Scaled Normalized Expression
sample (GOI)
Normalized Expression
sample (GOI)
Normalized Expression
Lowest sample (GOI)
------------------------------------------------------------------------------------------ =
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)
--------------------------------------- =