03/07/2021

Samples

Legend	Name	Description
A	Load Methods	Presents three alternatives to obtain the input data. These methods are also applicable for GPL and Raw data.
B	Web Items	Samples are loaded from the internet according to their GSM codes.
C	Local Files	Loads the samples from files located in a specific directory. Any file type can be used as input, as GEAP separates the file formats.
D	Library Items	Choose one or more samples among the saved library data.
E	Add/Remove GSM Code	Adds or removes a GSM code from the list.
F	List of GSM codes	List of samples identified by their GSM. The samples in this list will be downloaded from the GEO datasets.
G	Load Probe Information (GPL)	Loads the additional attribute columns that describe each the microarray probes. This option also loads the Platform metadata from Web or Library when checking these options.
H	Analyze RAW Data	Indicates preference for analyzing RAW data. It also determines the obtention method for probe-level annotations and package dependencies.
I	Advanced methods of data obtention	Additional options to load arrays from specific manufacturers.
J	Reload	Restores the checked files from the last session and displays the available options to reload them
K	Load	Begins the pre-analysis with the user-defined parameters.

Legend	Name	Description
A	Add or remove files in the list
B	List of files to be loaded from the local computer

Legend	Name	Description
A	Library entries	Entries in the library that can be included in preanalysis.

Legend	Name	Description
A	Allow CDF Package Download	When loading Affymetrix datasets in their RAW format, a CDF package may be required. This option will include the respective package in the download queue (e.g. "hgu133plus2cdf" for HG-U133 Plus 2). Note that this option will be ignored if the "Web" load method is not marked for RAW analysis.
B	Allow Probe Sequences Download	When loading Affymetrix datasets in their RAW format, this option will include the "probe" package in the download queue (e.g. "hgu133plus2probe" for HG-U133 Plus 2), which is required for GC-RMA and Plier options of statistical treatment. Note that this option will be ignored if the "Web" load method is not marked for RAW analysis.

GEAP