03/07/2021

Analysis Session

Legend	Name	Description
A	Session identifier	Primary session identifier. Example: GSE123456 for Series or GCT123456 for Custom Tables
B	Series overview	Displays the series' title, organism, platform, submission/update date, and summary. This menu is only displayed if the series' metadata from GEO was also loaded.
C	Actions tab	Basic actions for the current analysis session.
D	Information tab	Information related to the dataset itself, including metadata and processing parameters.
E	Stored files tab	Directory tree of temporary files stored in the current session.
F	Session properties	Opens a table of properties describing the functional state of the current session. Not intended for the regular User, but useful for debugging purposes.
G	Save project	Saves the current session in the current project or inside a new project.
H	Export tables	Exports one or more data tables from the current session according to the User's specification.
I	Save tables in Library	Saves one or more contents from the current Session to the Library.
J	Generate R Code	Generates the R source for the current session. The attached files related to the processed data can be exported in addition to the source code.
K	View Data Table	Opens the Data Table Browser to navigate the processed array values.
L	Quality analysis	Opens a dialog with parameters for Quality Analysis
M	Differential expression analysis	Presents the methods of Differential Expression analysis

Legend	Name	Description
A	Information type tabs	Tabs for the tables with dataset information, where each tab represents an information type. The possible information types are Series, Samples, Platform, RAW, and Treatment.
B	Table of information contents	Represents the contents of a stored data type, separated by attribute keys and values. _{Example: Series title (attribute) - My impressive experiment (value)}
C	Data table	Opens the Data Table Browser to navigate the processed array values.
D	Copy all	Copies the contents of the information table to the ClipBoard.
E	Export	Exports the information table to a tab-delimited file. Not to be confused with the Export Tables in the Actions tab.

Legend	Name	Description
A	Temporary directory tree	Directory tree of temporary files stored in the current Session. Right-click to display a context menu to copy these files or to navigate to the temporary folder. Note that this folder is deleted at the end of a Session or upon closing GEAP.

Legend	Name	Description
A	Property grid	Grid view listing the current Session's properties. These values are read-only.
B	Property description	Displays a brief description when selecting a property in the grid.

Legend	Name	Description
A	Output file format	The selected output format by which the file is going to be export
B	Include series contents	If checked, includes the table of values that correspond the series
C	Include samples	If checked, includes the metadata that describes the samples
D	Include platform contents	If checked, includes the table of values that correspond the probe descriptors
E	Include raw matrix	If checked, includes the concatenated table that represent the raw values
F	Include individual sample tables	If checked, each sample column will be exported separately
G	Concatenate the contents into a single file	If checked, there will only one output file that stores the entire exported data
H	Include headers and metadata	If checked, appends the metadata above each data table

Depending on the selected format, some options may become disabled or even be mandatory due to the own format's requirements.

Legend	Name	Description
A	Save as Series	If this option is selected, the current series will be saved as a GEO entry
B	Save as Custom Table	If this option is selected, the current series data will be saved as a custom table
C	Format name	The name of the data entry that will appear when selecting this series in the library
D	Include GEO series metadata	If checked, the series metadata will be included in the library. If there is an existing metadata for this GSE in the library, they will be overriden
E	Include GEO sample metadata	If checked, the samples metadata will be included in the library. If there is an existing metadata for these GSM in the library, they will be overriden
F	Include Raw data and treatment info	If checked, the metadata for raw and treatment will be included in the library
G	Save samples individually	If checked, saves the samples in different GSM entries. The the inner checkbox defines whether to attach each metadata in the saved entries
H	Save platform	If checked, includes the probe attributes. These can be the either the main table (Content), the metadata (Platform info), or both
I	Raw data matrix	If checked, the raw matrix will be saved in the library
J	Save annotation package for Raw data	If checked, one or more probe packages used to load the raw data will be saved in the library

Legend	Name	Description
A	New code	The newly created custom table identifier
B	Table name	The title that appears for the custom table in the library
C	Array type	Experimental method that describes this dataset (e.g. Expression Profiling by Array)
D	Organism	The scientific name of the organism used in this experiment
E	Description	A brief description of the experiment that used this dataset

Legend	Name	Description
A	Included samples	Samples to be included in the quality analysis.
B	Include/Exclude arrows	Include or exclude the sample from the analysis.
C	Excluded samples	Samples that will not be included in the analysis.
D	Heat map colors	Defines the color for the distance between samples represented in the heat map.
E	Log-scale	Perform the analysis using the values in log2 scale.
F	Restore	If an analysis was performed in the current session, restores and displays the results again.
G	Analyze	Starts the array quality analysis.

GEAP