| Microarray One Channel Regression |
| See Also |
This menu can be used to estimate effects using a separate regression analysis for each probe
from the between slide/chip differences. The expression values are obtained either by reading
a series of Affymetrix CHP files and the chip information from a CDF file, or by processing a
series of CEL files using the calculate Affymetrix expression values menu.
Before running this analysis, the expressions can be further normalized using the
one channel quantile normalization menu.
The analysis for the menu is performed using the MAREGRESSION
procedure which performs a regression to analyse the expression values for each probe.
The parallel regression menu is a more general form of this menu.
The results can be saved into structures by specifying the identifier names using the
store dialog which can be opened by
clicking on the Store button.
Available Data
This lists data structures appropriate for the edit box which
currently has focus. You can double-click a name to enter it in the
edit box.
Data Format
The data can be supplied in either of the following formats:
- Single Variate for Expression with Slide Factor - All the log-ratios are stacked
into a single variate, with factors that index the slide and probe/gene
- Pointer to Expression Variates for each Slide - Each slide has its data in
a variate, and a pointer which points to this set of variates is provided. The Slides
factor is not required, but if supplied it should just have one entry for each slide in the order of
the variates in the pointer. The Probes/Genes factor is that for a single slide, and
all slides must have a common layout.
The spreadsheet stack and
unstack menus can be used to reorganise the data
between these two formats.
Expression
A variate containing the expressions to be analysed, or a pointer to a set of variates
containing the expressions for each slide. The variates must all contain the data
in the same order.
Slides
The factor that identifies the slides. If the data are within pointer format, then this
should have just one entry per slide. If the data are within variate (stacked) format,
then this factor indexes the slides in the log-ratio variate.
Probes
The factor that identifies the probes or genes. If the data are within pointer format, then this
should contain the information for a single slide, and all the slides log-ratios are expected
in this common order. If the data are in variate (stacked) format, then this factor indexes the probes
in the expression variate.
Slide Order Validation
A factor the same length as the factors/variates within the Regression Model which indexes the slides.
This must have the same levels/labels as the Slides factor, and is used to
verify that the treatments are in the same order as the data specified in the expressions.
Supplying this factor is optional, but highly recommended to validate whether the data and
model terms match as expected. If the labels of the slides and check factor match, but are in a
different order, the model terms will be sorted into the correct order with a warning.
Regression Model
A formula specifying the combinations of factors and variates describes the regression model for
the series of slides. For a simple linear regression this will just be the name of the
variate that specifies the level of independent variable used on each slide.
See the page on model formulae for more details on how
to specify regression models.
Weights
A variate specifying the weights for each of the units in the regression.
If field is left blank then equal weights of 1 will be used.
Offset
Variate holding values to be used as an offset on the linear predictor scale.
An offset is used to take account of a fixed contribution to the linear effects for each unit.
If no offset is required then this field should be left blank.
Operators
This provides a quick way of entering operators in the regression model formula.
Double-click on the required symbol to copy it to the current input field. You can also type
in operators directly. See model formula for a
description of each operator.
Action Buttons
| Run | Run the analysis. |
| Cancel | Close the menu without further changes. |
| Options | Opens a dialog where additional options and settings can be
specified for the analysis. |
| Defaults | Set the menu settings back to the default settings.
Clicking the right mouse on this button produces a pop-up menu where you can choose to set
the menu using the currently stored defaults or the GenStat default settings. |
| Store | Opens a dialog to specify names of structures to store the results from the analysis.
The names to save the structures should be supplied before running the analysis. |
See Also