Custom Tables
| Legend | Name | Description |
|---|---|---|
| A | Series name | Name used in the loaded session |
| B | Advanced options | Presents advanced options for custom table building |
| C | Edit Metadata | Opens a metadata editor for the custom table |
| D | Load data | Loads one or more files in table-delimited format. Numeric values (e.g. amount of expression) and textual columns will be processed separately. |
| E | Load attributes | Loads one or more tab-delimited files. The loaded columns will be processed as attributes for the custom table. |
| F | 1st row = sample names | The first row will be used as the sample names. If unchecked, the program will give arbitrary names to the columns. |
| G | 1st column = probe names | The probe names will be located in the first column. If unchecked, the rows will be identified by their numeric order only. |
| H | Custom table | Loaded columns used for the custom table |
| I | Remove columns | Removes one or more selected columns |
| J | Load | Begins loading the custom table contents. |
Advanced Options
| Legend | Name | Description |
|---|---|---|
| A | Decimal separator | Character used to separate decimals, such as dot or comma |
| B | Tabulation separator | Defines which character is delimiting the cells within a row. The Tab is the default character used in tab-delimited TXT files |
| C | Index repeated attribute values | Optimizes the attribute columns by indexing the repeated entries. Suitable for columns containing many repeated values and few unique values |
| D | Multiple fields in attribute cells | Splits the cells containing a specific separator into composite cells. |
| E | Prefixes for ignored lines | If checked, all lines starting with one of these prefixes are ignored when reading a custom table file |
Remarks
Composite cells
The option "Multiple fields in attribute cells" splits the fields delimited by a specific separator. This option is suitable for attribute columns containing multiple fields, since the composite values will be recognized by GEAP as separate values. It allows, for instance, to filter the cell values separately from a DE results table.
Metadata Editor
| Legend | Name | Description |
|---|---|---|
| A | Field names | Column to add/remove/rename/select fields that are loaded with the custom table |
| B | Selected field contents | Text box with the contents of the currently selected field |
Remarks
Some fields are always generated when creating a custom table (e.g., "accession_id" and "last_update_date"). Adding keys with these names will overwrite their default values.
Any text content is allowed in the metadata, except for the "accession_id" field where only upper-case letters and digits are accepted.
Channel Selection
| Legend | Name | Description |
|---|---|---|
| A | Foreground channel | List of columns representing the main part of the detected values |
| B | Background channel | List of columns representing the background part of the detected values |
| C | Channel 1 | List of columns that belong the channel 1 of their corresponding samples |
| D | Channel 2 | List of columns that belong the channel 2 of their corresponding samples |
| E | Load | Applies the channels defines and redirects to the treatment options |
Remarks
This step is only valid if there are columns representing background or separate channel intensities. If no one has such properties, this step can be skiped by just clicking the "Load" button.
Note that the number of items in both channels must be equivalent, except if no item is present in the background or second channel. The order is also important here, since each sample will be defined using the overlapped values from pairs of channels along the listed order.