2-D Plots of Microarray Data Options

2D Plots of Microarray Data Options

Title

The main title to appear at the top of the graph.

X axis Title

The title for the X axis of the graph.

Y axis Title

The title for the Y axis of the graph.

Symbol

The symbols to be used for plotting the points in the graph.

Display Key in plot

Display a key indicating the slides for a superimposed graph, or the Groups within Plots factor levels. This item is ignored for the Trellis plot option.

Plot spline smoothed mean

Add the curve fitted by a cubic smoothing spline to the plot of Y on X. Using the command language this could be calculated as follows:

CALC SMean = SSPLINE(Y;X;12)

Plot Approximate Confidence Limits

Plot smoothed confidence limits that will approximately cover 95% of the values if the data were normally distributed about the smoothed mean curve. This could be calculated using the command language as follows:

CALC SMean = SSPLINE(Y;X;12)
CALC SRes = (Y - SMean)**2
CALC SRes = SQRT(SSPLINE(SRes;X;12))
CALC Lower,Upper = SMean + (-2,2)*SRes

Reference Line

There are three options on whether to add a reference line to the plots:

None	Don not add a reference line to the plots.
Zero	Add the zero reference line Y = 0 to the plots.
1-1	Add the 1-1 reference line Y = X to the plots.

Layout

There are three options on how the individual XY plots for each slides are laid out on the page:

All slides superimposed on a single plot	A single plot will be produced containing points from all slides, with the different slides points displayed in differing colours (which recycle after 50 slides).
Single plot per slide	Each slide will be plotted on its own page
Plots within grid layout on single page (Trellis)	The plots of each slide will be separate panels on a single page (although new pages will be produced when the number of panels exceeds the Rows and Columns settings.

Use Common scaling

When plotting graphs on separate pages with the Single plot per slide option, use the same X and Y range on all axes.

Rows and Columns

When plotting graphs on single page with the Plots within grid layout on single page (Trellis) option, use a grid containing the specified number of rows and columns to hold the graphs.

Action Buttons

OK	Store the settings and close the dialog.
Cancel	Close the dialog without making any changes.
Defaults	Set the options to the default settings.