Contents
Using
experiment sets, you can save a group of arrays
you access frequently when viewing or clustering data. In additional,
experimental sets are used to group array data within the context of a
publication. This help page describes how to create and use
experiment sets.
Sets can be used for several purposes:
- They can be used to organize experiments more flexibly than either
just category or subcategory (the only restriction is that the arrays
be from the same organism).
- They can serve a similar purpose as ArrayLists, but can be shared
with the group/public without need of a local UNIX account.
- They facilitate a more accurate documentation of the experimental design
for a set of hybridizations.
- They can help assist in data organization prior to publication.
Using the
Advanced
Results Search, select your desired search parameters and click
"Data Retrieval and Analysis". On the subsequent Search Results page,
select all experiments (from one organism, only) you want to organize
and click "Create Experiment Set". The selected experiments are
placed in the right box on the Experiment Set Organization page. The
order within the 'Experiments Included within Set' box, from top
(first) to bottom (last) is the order that experiments will be
displayed and clustered (if experiment re-ordering is not specified
during clustering). Using the various buttons you can:
- Order all your selections alphabetically either ascending (Sort
Asc) or descending (Sort Desc)
- Move selected individual or groups of experiments up or down,
ordering within the 'Experiments Included within Set' box.
- Remove unwanted experiments (or hold them for later re-addition)
within the 'Removed Experiments' box using the 'Remove (All)' and 'Add
(All)' buttons.
After achieving the desired order of arrays within the 'Experiments
Included within Set' box, click one of the following submission buttons.
- Select Experimental Factors
- Selecting experimental factors is
recommended for those sets that are destined for publication, or
indeed any set where the experimenter wishes to fully document the
experimental design, including experimental factors, factor values,
and measurements.
- Save Experiment Set
- By clicking the 'Save Experiment Set' button, the experimental
factor selection step is omitted, and the user skips to the final
step, Experiment Set Annotation
Experimental factors can be selected after organization of the
experiment set (prior to the final set annotation), or by editing an
existing experimental set. Experimental factors are the dependent and
independent variables of the experiment itself (Ex. time, glucose
concentration, disease state, etc.) Each time experimental factors
are associated with an experiment set, three may be designated. If
more than three are required to fully explain the experimental design,
then the newly created set must be edited, and additional factors added
as required.
- Selecting Experimental Factors and Descriptions:
- First, choose the experimental procedure or design that contains
the experimental factors which the set is organized from the first
column's menu.
- Next choose the experimental parameters from the second column's
menu. This will be the experimental factor, whose value is often
systematically varied among the arrays contained within the set. If
the experimenter had previously annotated the individual array's
experimental parameters, these parameter/factor values will be
pre-filled within the final annotation step. For more on pre-association
of an array's procedural details, please consult the helpfile on entering procedural annotation or
edit the details of each array (via Display Data).
- If the factor chosen is not sufficiently descriptive of the
experimental design, or if it requires either qualification or
contextual explanation, supply a description of the experimental
factor within the textbox immediately below to the factor menu.
- Measurements: If your chosen experimental factor
has a measurement (i.e. it will likely have a value with associated
units for all arrays), then select the unit kind, default unit, and
unit type from the pop-up menus in the far-right column.
- If your factor is not measured, make certain the
top units-menu in that row is set to "Not measured".
- The default unit selected can be altered on a per array basis on
the next step. Do not fret if the unit doesn't apply to all arrays
within the set. Unit kinds (time, concentration) and types (absolute,
relative), however, do apply to all arrays.
- If the appropriate unit kind or default unit is not available
within the pop-up menus, please suggest to the database
curators that your unit of choice be included.
Once the experiment order has been established for the set, and the
experimental factors have been selected (optional), now the
appropriate annotations need to be made.
- First and foremost, an appropriate Experiment Set Name
(required) must be entered.
Currently, the only method of returning experiment sets is by name,
through the Basic
Search. Therefore, it is important that a succinct,
self-explanatory name is chosen (try not to be arbitrary or
ambiguous). Please use these guidelines in order to optimize the
query/display within the Basic Search:
- Try to limit the name to 60 characters (max 100).
- The organism does not need to be included within the Experiment Set Name.
- Keep it succinct (use the Description field (below) for your elaborate details).
- Longevity: As there is a need for temporary
worksets of data, you can choose to make the set permanent, or
self-removing (after a couple weeks).
- Experiment Set Design (required) - Experiment Sets are
required to be classified as a specific type, in order allow better
display of the contents.
- Replicate : Biological - This set type is for
repetition of the experiment prior to extracting mRNA (typically) for
analysis. These sets are meant to assay the reproducibility in
biological experimental conditions.
- Replicate : Technical - This type is for an
repetition of experimental conditions after mRNA extraction. This
includes probe labeling, hybridization, and reverse duplicates.
- Logical Grouping - This type describes to
experiments that "logically" go together when viewed within a larger
context (similar to Categories encompassing subcategories).
- Time Course - A set of arrays where the primary
experimental factor is Time (temporal measurements). Often includes
an additional experimental factor, such as Compound Based Treatment,
Growth Conditions, or Developmental Stage.
- Dose Response - A set of arrays where the
experimental factor is a concentration measurement variable.
Often includes a Compound Based Treatment experimental factor.
- Clustering Weight : If the weight of an
experiment should be reduced (if it is represented more than once
within the set) or increased, enter the factor by which its weight
should be multiplied. For example, entering "0.5" would halve the
weight an experiment has on clustering. The default weight is 1.
- Factor Values : For each factor that was
selected, and for each array, the user can specify an optional value.
The factor value can be a text string or numeric. In the case of a
measurement it is intended that the value be a number only, as units
are found in the adjacent pulldown menu (if the factor was specified
as being measured on the previous step). For
example, for the array representing the 10 minute timepoint within a
Time Series set, enter 10 for that factor's value and
select m from the adjacent unit menu.
- Description : This field provides for the full,
exhaustive description that the experiment set name does not allow.
This field will be viewable within 'View Experiment Set' from the list
display. Think of this field as a figure legend or an abstract.
Once the experiment set has been created, the experiments contained
can be displayed and clustered within the set's context. Currently,
the only method of returning experiment sets is through the
Basic
Search. To either display or analyze experiment sets, within the
"
Pick results type" section at the top of the Basic
Search page select one of the following:
- My Experiment Sets : limits the browsable select
lists to the sets you created. Hence, this option is limited
to internal researchers.
- Experiment Sets : lists all viewable experiment
sets, by organism, within the browsable select lists.
As in the advanced search, there are two choices to retrieve the data:
- Display Data (table list): This search submission
will return the experiment contents of the experiment set, as well as
optional links to view and edit/delete the experiment set details
(creator only).
- Data Retrieval and Analysis: This Basic Search
submission is the launch point to begin data analysis. All the
experiments contained within the set are passed the directly to data
selection prior to clustering, as it is assumed the user wants the
analysis to be conducted within the context of the set's organization.
For further information on subsequent steps in clustering, see the
Advanced Results Search help.
For further information on the Basic Search, see the Basic Search
help.
Only the creator of the experiment set has the ability to add or
remove experiments, re-arrange the experiment order, or edit the set's
annotation. To edit a experiment set you own, use the
Basic
Search, choose the experiment set name from the select list, and
Display Data (as described
above). At the top of the resulting display page,
a header containing the set's Name, Organism, and Type are displayed,
along with its
Options. If you are the set's owner,
there is an
icon. Clicking on this icon will open a
pop-up window containing 4 editing options whose behavior is very
similar to the process of experiment set creation, detailed
above:
- Edit Experiment Set Annotation : use this option
to edit the name, experimental design, factor descriptions, factor
values, units, and description of the set (without changing the
experimental contents or order).
- Rearrange/Remove experiments from experiment set
: use this option to either remove unwanted experiments or rearrange
the order of experiments within the experiment set. In addition,
after you do this, you are allowed to either add/edit experimental
factors or edit the set annotation, if desired.
- Add/Remove Experimental Factors : choose this
option to either document additional experimental factors or delete
prior factors that were poorly conceived or annotated.
Note: deletion of experimental factors will remove
all previously associated factor values for all arrays if the changes
are commited upon the final annotation step.
- Add new experiments into experiment set : use
this option to add new experiments to the existing set from the
Advanced Search (limited to the set-specified organism). After
choosing the desired experiments and clicking "Edit Experiment Set",
the experiment additions are in the left box while
the pre-existing experiments in the pre-specified order are on
the right. Integrate the new experiments into the set by
clicking the "Add All" button and use the move buttons to re-order the
set, if needed. Saving the new set will pass you to Option 1 above,
allowing you to edit the set annotation, if desired.
The behavior of these three commands is very similar to the process of
experiment set creation, detailed above. As in set creation, you may
not introduce experiments from different organisms into the set using
"Add new experiments into experiment set".
Only the creator of the experiment set has the ability to delete the
experiment set. To delete a experiment set you own, use the
Basic
Search, choose the experiment set name from the select list, and
Display Data (as described
above). At the top of the resulting display page,
the experiment set header contains the
Options. If
you are the set's owner, there is an
icon.
Clicking on this icon will
remove the experiment set organization and annotation, but will leave
the experiments intact.
- Currently experiment sets may only include experiments
from a single organism.
- Both the interactive ordering/movement of arrays within
Experiment Set Organization and the heirarchical menus of
procedures/parameters and measurement-kinds/units with experimental
factor selectionrequires JavaScript be turned on in
the web browser.
- For Netscape Navigator/Communicator:
- On the Edit menu, select Preferences.
- Under Web Browser, click Web Content.
- In the Active Content area, select the 'Enable scripting' check box.
- For MS Internet Explorer:
- On the Edit menu, select Preferences.
- Click Advanced.
- Select 'Enable JavaScript'
There are
required fields within Experiment Set
Creation. You must specify the
Experiment Set name,
and the
Classification.
If you specify your saved set as
temporary, it will be deleted
after two weeks.
