Table 2

Comparison of HDBStat! with other software packages. All these software packages are still in active development and new functions will undoubtedly be added over time.
	HDBStat!	SAM	BRB-Array Tools 3.2.2	TM4

Two color data handling	Common reference and balanced block designs	No	Yes	Yes

Database	No	No	No	Yes

Ratio Statistics	Yes	No	Yes	Yes

Normalization	Yes	Yes	Yes	Yes

Max number of arrays	No limit	255	249	No limit

Discriminate Analysis	No	No	Yes	Yes

ANOVA	Yes	No	Yes	Yes

Bootstrapping	Yes	Yes	Yes	Yes

Non-normal and heteroskedastic data handling	Yes	Yes	Via normalization	Via normalization

Non-parametric statistics	Yes	No	Yes	No

Cluster analysis	No	No	Yes	Yes

FDR (number)	8	1	2	1

Family Wise Error rate corrections	2	0	1	1

Quality Control	Yes	No	No	Yes

Power Analysis	Yes	No	No	No

Automatic report generation	Yes	No	Yes	No

Gene Class testing	No	No	Yes	No

Automatic Annotation	No	Link out	Yes	No

Platform	Single program implemented in Java & available via Java Web Start technology	Microsoft Excel Add-in	Microsoft Excel Add-in	4 separate programs, 3 of which implemented in java & 1 in C++

Trivedi et al. BMC Bioinformatics 2005 6:86 doi:10.1186/1471-2105-6-86