Table 1.

Functionalities comparison between COMMAND>_ and other tools used to collect gene expression data from public databases

Tool	R	Local	GUI	GEO	AE	SRA	DB	ANN	Search	Note
COMMAND>_	NO	YES	YES	YES	YES	YES	YES	YES	YES
GEOquery	YES	NO	NO	YES	NO	NO	NO	NO	NO
ArrayExpress	YES	NO	NO	NO	YES	NO	NO	NO	YES
GEOmetadb	YES	NO	NO	YES	NO	YES	NO	NO	YES	requires the dowload of an sqlite file with meta information
SRAdb	YES	NO	NO	YES	NO	YES	NO	NO	YES	requires the dowload of an sqlite file with meta information
compendiumdb	YES	NO	NO	YES	NO	NO	YES	NO	NO
virtualArray	YES	YES	NO	YES	YES	NO	NO	NO	NO	allow to normalize data and correct for batch effect, available only for Bioconductor <= 2.14
Microarray retriever	NO	NO	YES	YES	YES	NO	YES	NO	YES	unavailable

Each column represent one functionality, respectively: R (the program is an R package), local (the program allow to use local data), GUI (the program provides a Graphical User Interface), GEO (the program connects to GEO), AE (the program connects to ArrayExpress), SRA (the program connects to SRA), DB (the program provides a database to store expression data), ANN (the program allows to annotate probes), Search (the program allow to perform queries using free text besides accession id) and Note (the program has special features or limitations)