2.2 Samples menu

Each experimental condition sample is represented by a hybridized sample (abbreviated HP in MAExplorer). The Samples menu operations include operations to select the current hybridized sample or samples. The simplest model of a MAExplorer analysis assumes (at least) two microarray hybridized samples variables HP-X, HP-Y whose data may be plotted against one another or compared. The default is a single HP-X sample and a single HP-Y sample.

The first menu command, "Choose HP-X, HP-Y and HP-E samples", entries lets you change the current working HP-X 'set', HP-Y 'set', and HP-E 'list' hybridized samples.

The second menu command, "Choose named condition lists of samples", lets you define or edit new named lists of hybridized samples. This is useful for defining sets of replicate samples. These may be further manipulated using the (Edit menu | Sets of Conditions (samples)) commands.

The third menu command, "Choose ordered lists of conditions", lets you define or edit new named Ordered Condition Lists (OCL) of named condition lists. This is useful for defining a sub-experiment consisting of N conditions each with replicate samples. The last OCL manipulated is defined as the "current OCL". The current OCL is used in the OCL F-test Filter.

The fourth menu command, "Set Samples from lists", lets you change the current HP-X and HP-Y, HP-Y samples as well as the HP-X 'set', HP-Y 'set', and HP-E 'list' samples. This is similar to using the "Choose HP-X, HP-Y and HP-E samples" command, but is more dificult to use. You may change the current HP-X or HP-Y sample by clicking on the sample name directly in the list of sample names on the left side of the pseudoarray image (see Figure 2.2.3 legend).

The fifth menu entry, "Edit use (Cy5/Cy3) else (Cy3/Cy5) for each HP", lets you swap data channels for Cy3/Cy5 data for individual samples.

Other menu commands list the status of the current HP-X 'set', HP-Y 'set', or HP-E 'list', and define condition class names that are associated with the HP-X 'set' and HP-Y 'set'. The last menu entry, "Use HP-X & HP-Y 'sets' else single samples", lets you switch between using HP-X and HP-Y as single samples of sets of multiple samples. For example, if you are using a scatter plot of X and Y, it will switch the data being plotted from a comparison of single samples to a comparison of means of sets of samples depending on the status of the switch. Sets of samples are used extensively in data explorations.

Figure 2.2.1 shows setting the HP-X, HP-Y, HP-E lists of samples using the "Chooser" - the preferred method. Figure 2.2.2 shows setting the HP-X sample from the menus. Figure 2.2.3 shows changing the current HP-X sample by clicking on a sample name in the microarray image.

Choosing the X and Y sets of samples and the E ordered list of samples

Figure 2.2.1 Samples menu - selecting lists of samples by using the "chooser". The hybridized samples assigned to the current HP-X, current HP-Y, set of HP-X, set of HP-Y and expression profile list HP-E may be changed from the Samples pull down menu using the Choose HP-X, HP-Y and HP-E option lets you graphically change the currently active sample HP-X, HP-Y sets and E-list.

Selecting HP X, Y, or E samples using the pull-down menus

Figure 2.2.2 Samples menu - selecting samples by source characteristics. The hybridized samples assigned to the current HP-X, current HP-Y, set of HP-X, set of HP-Y and expression profile list HP-E may be changed from the Samples pull down menu. The specific "By Source" menus shown here are from the MGAP database. This figure shows the user changing the current X sample from the developmental stages submenu that is part of the "By Source" submenu. Alternatively, samples containing a keyword or part of a keyword can be found using a "guesser" popup window that allows the use of wild cards. This is invoked using the "From list of all H.P.s" submenu. For example, you could specify "*pregnancy*" to find all samples of containing that word.

Switching current X or Y sample by clicking on desired sample in list at left edge of pseudoarray image. Switch between X and Y by toggling '[X]' and '[Y]' of the Current Sample box.

Figure 2.2.3 Changing the current sample to either the HP-X or HP-Y sample by clicking on a sample name at the left edge in the microarray pseudoarray image. The current sample is indicated in magenta. Click on the magenta "*" adjacent to the new name you want to select and it will change the HP-X sample. To switch between setting HP-X and HP-Y, click on the [X] Current Sample box to change the sample to HP-Y. You can click on [Y] Current Sample box to change it back to HP-X. Then clicking on a sample name will set it to the current HP-X or HP-Y that was selected. This figure shows that the user had selected [Y] and C57B6-L10-29hrs for the new HP-Y sample.

2.2.1 Selecting hybridized samples with Chooser or pull-down menu sample lists

The Set Samples from lists submenu lets you define HP-X, HP-Y, HP-X 'set', HP-Y 'set', or HP-E 'list' from lists of samples. It contains four submenus:

The Set current HP-X sample and Set current HP-Y sample commands offer another way to set the single current X and Y sample (see Figure 2.2.3 above for the preferred way using the "Chooser").

The Edit HP-X & HP-Y 'sets' of samples by source menu allows the user to define HP-X and HP-Y as sets having multiple hybridized samples. Then, the mean values of the genes are used when comparing HP-X with HP-Y.

The Edit HP-E expr. profile 'list' by source menu allows the user to define an ordered list of samples for use in expression profile statistics. Then, an expression vector of normalized quantification values (one for each sample in the HP-E list) is computed for each gene. Note: to place the samples in a particular order, start with an empty HP-E set and then add them in the order you desire.

The Convention for pull-down menu sample selection lists

We use a common sample selection scheme when selecting a sample from a pull-down menu list. This sub-sample "By Source" option is only available if your database was set up to allow sub-sample source names in the Samples database.

For example, the By Source database-specific entries for the MGAP database includes the following submenus.

The From list of all samples selection pops up a hybridized sample guesser dialog window. As with the gene name guesser, you can start typing in the name of a sample and it will give you a list of HPs that match that initial string. You then click on the sample you want and then press the Done button.

2.2.2 Swapping selected samples' (Cy3,Cy5) channels in ratio data dye-swap experiments

The Edit use (Cy5/Cy3) else (Cy3/Cy5) for each HP command may be used to selectively swap (Cy3,Cy5) data entries so the user may use the samples (carefully, since gene labeling efficiency is not always symmetric!) dye-swap data for replicates. This is only available for ratio data. It swaps the data contained in MAExplorer (memory only) so that the Cy3 data is swapped for the Cy5 data. For example, consider the case where there are two materials A and B hybridized in two experiments and labeled as follows: E1 (A=Cy3,B=Cy5) and E2 (A=Cy5,B=Cy3). Then, assuming uniform symmetric labeling (which is generally not the case - although it might be true for a subset of genes), then one might average data from E1 and E2 if the data from E1 (or E2) were swapped. This is shown in the following figure.

Selectively swapping (Cy3,Cy5) for particular samples

Figure 2.2.4 Samples menu - selectively swapping (Cy3,Cy5) data channels for particular samples. This is only operative if your database contains Cy3/Cy5 ratio labeling data. This is useful in databases containing subsets of dye-swap experiments mixed in with other samples that are not dye-swapped.

2.2.3 Viewing sample HP-X, HP-Y, and HP-E partitions

You setup sets of HP samples for the HP-X and HP-Y sample sets and HP-E expression list of samples using the Chooser (above). The current contents of these lists may be viewed using the List HP-X & HP-Y sample 'sets' to list the samples in the HP-X and HP-Y 'sets'. The List HP-E sample 'list' may be used to list the samples in the ordered HP-E 'list'.

2.2.4 Defining sample condition 'class' names

When using sets of conditions, the HP-X and HP-Y 'sets', you will probably want to assign meaningful names to these sets. The commands Define HP-X class name and
  • Define HP-Y class name assign a free text line name for the sets.

    2.2.5 Toggling between single HP-X (-Y) samples and HP-X (-Y) sets

    When MAExplorer first starts up, it assumes that you wish to treat the data as single samples so that HP-X and HP-Y are assigned to single samples. However, if you want to work with sets of multiple samples then you must toggle the state using the Use HP-X & HP-Y 'sets' else single samples [CB] check box command. This toggles the state between treating the data as multiple samples (HP-X and HP-Y 'sets') or as single HP-X and HP-Y sample samples.

    2.2.6 Create and edit named condition lists of samples

    The command Choose named condition lists of samples lets you define new or edit existing named lists of hybridized samples called "Condition lists". Associated with each condition list is a set of annotation parameters to document the condition. The condition lists may be used in the (Edit | Sets of conditions) operations. Among other operations, you may assign any condition list to the working HP-X 'set', HP-Y 'set', or HP-E list of samples used through MAExplorer. The last condition list that was edited with the (Sample menu | Choose named condition lists of samples) is called the "current condition" that could be used in various operations. Figure 2.2.5 shows a screen illustrating a popup condition chooser session where the legend describes the options.

    Editing named condition lists of samples

    Figure 2.2.5 shows a screen illustrating a popup condition chooser session. The set of all samples in the database is in the scrollable "Remainder Samples" window in the upper left. The samples you have selected for the condition list being edited is shown in the upper right "Selected Samples in current condition" window. The list of all conditions in the database is in the lower left "List of Conditions" window. The current condition list that is selected is highlighted and its contents displayed in the "Selected Samples" window. User defined annotation associated with the current condition are displayed in the right "Current Conditioned Annotation" window. To add a new condition, click on the Add Cond button to define the new condition name. The Remove Cond button is used to delete a named condition list. The List Cond button pops up a report listing the samples and annotation for the current condition. The List All button pops up a report listing the the names of all of the conditions and the annotation names. You may add or remove new annotation names for all of the conditions. The Add Ann button will add the new annotation you enter into all conditions - you must enter the data for each condition that requires it. You may The Save the current status of all of the conditions into your working database. If you have pressed Cancel before saving, then you will not have saved your edits. Pressing the Done button will save the changes and pop-down the window.

    2.2.7 Create and edit named ordered condition lists (OCL) of conditions

    The command Choose ordered condition lists of conditions lets you define new or edit existing named ordered lists of conditions called "Ordered Condition Lists" (OCL). Associated with each ordered condition list is a set of annotation (name, value) pairs to document the condition. The last condition list that was edited with the (Sample menu | Choose ordered lists of conditions) is called the "current OCL". The current OCL is used by the (Filter menu | Filter by current Ordered Condition List (OCL) F-Test [p-Value] slider [RB]) test. Figure 2.2.6 shows a screen illustrating a popup ordered condition list chooser session.

    Editing named ordered condition lists (OCL) of samples

    Figure 2.2.6 shows a screen illustrating a popup ordered condition list (OCL) chooser session. The set of all conditions in the database is in the scrollable "Remainder Conditions" window in the upper left. The conditions you have selected for the OCL being edited is shown in the upper right "Selected Conditions in current OCL" window. The list of all conditions in the database is in the lower left "List of Conditions" window. The current OCL list that is selected is highlighted and its contents displayed in the "Selected Conditions" window. User defined annotation associated with the current OCL are displayed in the right "Current OCL Annotation" window. To add a new OCL, click on the Add OCL button to define the new condition name. The Remove OCL button is used to delete a named condition list. The List OCL button pops up a report listing the conditions and annotation for the current OCL. The List All button pops up a report listing the the names of all of the OCLs and the annotation names. You may add or remove new annotation names for all of the OCLs. The Add Ann button will add the new annotation you enter into all conditions - you must enter the data for each condition that requires it. You may The Save the current status of all of the OCLs into your working database. If you have pressed Cancel before saving, then you will not have saved your edits. Pressing the Done button will save the changes and pop-down the window.