How do I use tags?

Note: this page describes tagging in Progenesis SameSpots v4.1 and later. If you're using SameSpots v4.0 or earlier, please refer to the old tagging FAQ.

Tags are one of the most flexible analysis tools in Progenesis, allowing you to attach a label to a selection of spots. You can then show or hide spots using a filter that's based on a selection of their tags.

In this article:

• An example
• Creating new tags
• Applying and removing tags
• Renaming and deleting tags
• Filtering your spots

An example

For example, you could very quickly find spots whose expression is increasing significantly by doing the following:

1. Create a tag called "Significant" for all spots that have a low p-value
2. Create a tag called "High fold change" for all spots that have a Fold value greater than 2
3. Create a tag called "Up-regulated" for all spots that have their highest values in a Treated condition
4. Combine these tags in a filter, so that only spots that have all three of the tags are shown

Creating new tags

There are two ways to create new tags for your spots:

• Create tags for the selected spots
• Create tags for spots having particular values

Creating a tag for the selected spots

To create a tag for the selected spots, first select the spots to which you want to apply the tag. Spots can be selected in the list at the left of the screen.

To select a range of spots, you can click the spot at the start of the range, then hold down the Shift key and click the spot at the end of the range. To select or deselect an individual spot, hold down the Ctrl key and click on it in the list.

Next, right-click on any of the selected spots in the list. The tag menu will appear; from this, select the New Tag… option. The following window appears:

Enter the name that you want to give the tag. If you'd like it to have a different colour, click the coloured button to the left of the name. When happy, click OK. The tag is created and each of the selected spots is given that tag. If any spots already had a tag, the new tag is applied in addition to the existing tags.

Creating tags for spots having particular values

Using the QuickTags feature, certain types of tag can be created without first having to select spots. For example, you can quickly tag all spots with a p-value of less than 0.05.

To use QuickTags, right-click anywhere in the list of spots. In the tag menu, open the Quick Tags sub-menu and select one of the options in it. As before, the Create New Tag window will appear. Enter a name for the new tag and, optionally, choose a colour, then click OK. This time, the new tag will be applied to all spots that meet the criterion selected in the Quick Tags menu.

Note: if your spot measurements change, this tag will not be recalculated. That is, all spots that were assigned the tag when it was first created will continue to have that tag, regardless of their new measurements.

Applying and removing tags

To give an existing tag to a spot (or set of spots), simply select the relevant spots in the list, then either:

• right-click on any of the selected spots, or
• click the arrow in the Tag column header

Either method will display the tag menu. From that, simply select the tag you wish to apply or remove.

Renaming and deleting tags

If you need to rename a tag, or you want to delete a tag that you no longer need in your experiment, this can be done easily. Click on the arrow in the Tag column header and select Edit tags from the menu. The Edit Tags window appears:

To rename a tag, highlight it and click Rename tag to show the Rename Tag window.

To delete a tag, highlight it and click Delete tag. Note that this will remove the tag from all spots, not just the selected spots.

Filtering your spots

While labelling your spots with tags is a helpful way to organize your data, filtering based on those tags is the more powerful analysis tool. By creating a filter, you can quickly reduce the amount of data you are viewing, enabling you to concentrate on the spots of real interest.

To create a filter, click the Create button in the filter panel shown above each spot list. The Create a filter window appears:

In this window, you can build a filter showing:

• spots that have all of the tags in a given set
• spots that have at least one of the tags in a given set
• spots that have none of the tags in a given set
• or any combination of the above options

For example, imagine you have defined two tags: one for spots that have a p-value of less than 0.05; and one for spots that have a fold change of 2 or more. The Create a filter window would initially look as it does above. To show only the spots that have both of the tags, click and drag each tag in the Available tags list to the top list on the right. When the done, the dialog looks like this:

Only spots that have both of these tags will be shown when you click OK. All other spots will be hidden. Any tags left in the Available tags list will not affect the filter.

Here are some further examples of tag combinations you could use to filter your spots:

To show this…	…you could set up this filter (click to expand)
Spots that are at least 2-fold up-regulated in the Control group and have an Anova p-value of less than 0.05
Spots with a power of at least 0.8 and p-value less than 0.05, except those with a q-value above 0.01
Spots that have either a low p-value (less than 0.05) or a fold change greater than 2
Spots that have no tags assigned to them
Spots that have any of the tags assigned to them

Finally, to return to showing all spots, just click the Clear the filter button and click OK.