This menu can be used to calculate the medians of probe expression values
across a series of slides. The median expression level for each slide
is estimated and removed in a iterative fashion using an algorithm called
the median polish algorithm. An approximate standard error of the mean
can be calculated which is defined as 1.483 times the median absolute
deviation from the probes median.
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 Intensity with Slide Factor - All the log-ratios are stacked
into a single variate, with factors that index the slide and probe/gene
- Pointer to Intensity 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 given 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
The expression values to summarize.
Use Log (base 2) Transformation
The Expression variate is log 2 transformed before summarizing it.
The calculation for this using GenStat's command language is:
CALC LogY = LOG(Y)/LOG(2)
Slides
The factor that identifies the slides. If the data are in a pointer format, then this
has just one entry per slide. However, if the data are in a variate (stacked) format,
this factor indexes the slides in the intensity variate. This item is not
required when a pointer is specified.
Probes
The factor that identifies the probes or genes on a slide. If the data are in pointer format, this
has just one entry per probe, but if the data are in variate (stacked) format,
this factor indexes the probes in the expression variate.
Save
These items specify the data to be saved from the analysis.
| Probe IDs | text |
the probe labels to index the results. |
| Median Expression | variate |
the median expression level for each probe. |
| Standard Error of Median | variate |
the approximate standard error of the median expression level for each probe. |
Display in Spreadsheet
If this is selected, the saved results will also be displayed within spreadsheet windows.
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 shortcut menu where you can choose to set
the menu using the currently stored defaults or the GenStat default settings. |
Example
A set of results from 9 Affymetrix chips is to be summarized.
The expression values have been created with the
Calculate Affymetrix Expression Values menu.
These are now to be summarized for each probe with the following menu:
The options used were set in the Options dialog:
This gives a spreadsheet containing the results:
See Also