Bio-Rad Firmware & Software Updates - Manual (Page 104)

MiniOpticon Instruction Manual
93
• 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 (C
q
) 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 run design:
• Unscaled expression. This option presents the unscaled normalized gene expression
• Highest expression. Scale the normalized gene expression to the highest for each
target by dividing the expression level of each sample by the highest level of expression
in all the samples. This scaling option uses the scaled to highest formula
• Lowest expression. Recalculate the normalized gene expression for each target by
dividing the expression level of each sample by the lowest level of expression in all the
samples. This scaling options uses the scaled to lowest formula
E RROR T YPE
Select an option for the type of error calculations (error bars) in the Gene Expression graph:
• Standard Error of the Mean (default, SEMs)
• Standard Deviation (Std Devs)
C HART E RROR B AR M ULTIPLIER
Select a multiplier for the error bars in the Gene Expression graph. Select one of these
integers: +/- 1 (default), 2, or 3. The type of multiplier changes when you select the Error Type:
• SEMs for Standard Error of the Mean
• Std Devs for Standard Deviations
T ARGET S TABILITY V ALUE
Target stability values can be calculated whenever more than one reference gene is used. The
software calculates two quality parameters for the reference genes:
• Coefficient of Variation (CV) of normalized reference gene relative quantities. A
lower CV value denotes higher stability
• M-value. A measure of the reference gene expression stability:
Table 34. Acceptable values for stably expressed reference genes
(Hellemans
et al. 2007)
Samples CV M
Homogeneous < 0.25 < 0.5
Heterogeneous < 0.5 < 1