Download Lucidea Microarray ScoreCard

Chapter 9 Comparing data from multiple slides
9.1.2 Sensitivity and Specificity
To assess the system sensitivity and to check for non-specific binding, use the
information in the Detection Limits table (section 8.4). The detection limit
signal information can indicate the sensitivity of the Microarray system and
the overall quality of each hybridization:
•
The lower the signal detected, the greater the sensitivity.
•
The higher the signal detected, the lower the specificity of hybridization.
The dynamic range controls (DRs) correlate with the relative abundance of the
mRNA spike and can indicate the expression level that can be detected. For
example, if dynamic range 6 (6DR) is not above the threshold signal level for
the detection limit, you can state with confidence that genes with expression
levels below the 6DR relative abundance are not detectable.
9.1.3 Gene Expression data Accuracy and Precision
To determine the accuracy and precision of the ratios, examine the Ratio
Analysis table (section 8.2) and the Ratio Precision table (section 8.3).
Consider the following when you inspect the information in these tables:
•
In the Ratio Precision table, the average standard deviation of the
normalized log ratio (Mean NLR SD) should be acceptable. Typically,
the values should be less than the default threshold value of 0.150.
•
In the Ratio Analysis table, the values of the normalized ratio and dynamic
range controls should be acceptable based on your threshold difference
from the target values.
•
The normalized log ratios (NLRs) may be less accurate when one or more
signals fall below the detection limit.
To assess the performance of the normalization process, see appendix A.
9.2 Interpreting the Gene Expression data from
single and multiple hybridizations
This section discusses how to use the output from Lucidea Microarray
ScoreCard to obtain gene expression ratios (n-fold up-regulation or
down-regulation) and how to combine data across multiple hybridizations.
p9-2
●
Lucidea Microarray ScoreCard User’s Guide