This tab provides a comprehensive summary of
ANOVA
model fitting results. It is important to keep in mind which
model
was fit and to carefully consider hypotheses of interest. Depending on the variability in your data and your objectives, you might wish to alter the significance criterion to obtain fewer or more significant genes. The numerous drill-down options available in the
Action Buttons
pane on the left-hand side are valuable for exploring interesting subsets.
The
Results
tab contains the following elements:
Volcano plots
are a convenient way to summarize a specific
hypothesis test
across all genes. Each plot is based on a single hypothesis of interest and each point in the plot is a gene. The
x
-axis represents a difference or estimate and the
y
-axis its corresponding
-log
10
(
p-value
). Volcano plots have a characteristic "V" shape because estimates near zero tend not to be significant and those away from zero tend to have smaller p-values / larger
-log
10
(
p
-values). Significant genes are those in the upper left and right quadrants of the plot, akin to exploding pieces of molten lava. The red dashed horizontal line usually represents a significant criterion computed by some multiple testing method like
FDR
. You can change this value with an action button in the left panel. You can also resize all of the plots with a slider above them.
This plot enables you to compare
expression
patterns for all significant genes simultaneously. The standardized least squares means for every gene that is significant in at least one volcano plot are clustered both horizontally and vertically and depicted with a heat map. The
standardization
is to
mean
0 and
variance
1, so the emphasis is on patterns and not overall expression. Each row of the heat map is a gene and each column is a distinct LS mean. You can see which genes and LS means have similar expression profiles. You can click on branches of the horizontal dendrogram to select all genes in that cluster. These genes are then highlighted in other plots and you can then click Action
Buttons
on the left-hand side for further analyses.
This tab provides a comprehensive summary of
ANOVA
model fitting results. It is important to keep in mind which model was fit and to carefully consider hypotheses of interest. Depending on the variability in your data and your objectives, you might wish to alter the significance criterion to obtain fewer or more significant genes. The numerous drill-down options available in the
Action Buttons
pane on the left-hand side are valuable for exploring interesting subsets.