4 - Central Institute of Brackishwater Aquaculture

National Workshop-cum-Training on Bioinformatia and Information Management in Aquaculture
For example, we have the following intensity ratio results for two replicates (A
and B) after normalization:
The mean of these replicates is 1.25 instead of 1, which would have been
expected. If the 2-based logarithmic transformation is applied, the log ratios are:
The mean of these log ratios is 0, which corresponds to the mean intensity ratio
of 1. Although log-transformation is not always the best choice for microarray
data, it is used because the other transformations lack this handy additive
property. One downside of the log-transformation is that it introduces systematic
errors in the lower end of the expression value distiibution.
3.2.3. Replicates: If the experiment includes replicates, their quality can be
checked with simple methods, using scatter plots and pairwise correlations or
hierarchical clustering techniquesewhen the distribution of the intensity values is
skewed, the median characterizes the central tendency better than the mean.
The median and mean can also be used to check the skewness of the
distribution. For symmetrical distributions mean and median are approximately
equal.
3.2.4.0utliers and Filtering bad & Uninteresting Data: Outliers in chip
experiments can occur at several levels. There can be entire chips, which deviate
from all the other replicates. Or there can be an individual gene, which deviates
from the other replicates of the same gene. Outliers should consist mainly of
quantification errors. In practise, it is often not very easy to distinguish
quantification errors from true data, especially if there are no replicate
measurements. If the expression ratio is very low (quantification errors) or very
high (spot intensity saturation), the result can be assumed to be an artifact, and
should be removed. Most of the actual outliers should be removed at the filtering
step (those that have too low intensity values). This is often equivalent to a
filtering, where observations with too low or high intensity values are excluded
from further analyses.
3.2.5. Linearity: Linearity means that in the scatter plot of channel 1 (red
colour) versus channel 2 (green colour), the relationship between the channels is
linear. It is often more informative to produce a scatter plot of the logtransformed
intensities, because then the lowest intensities are better
represented in the plot. In this kind of a plot, the data points fit a straight line, if