Use this to to control additional options and settings for the 2-D Plots of microarray data menu.

## 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 |
Do 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 |
Produces a single plot 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 |
Reset the options to the default settings. |

## Action Icons

Clear |
Clear all fields and list boxes. | |

Help |
Open the Help topic for this dialog. |

## See also

- 2D Plots of Microarray data
- Microarray menus
- Histograms
- Spatial Plot
- Volcano Plot
- TRELLIS procedure for trellis plots using command language