Friday, October 08, 2010

Free options for ANOVA

Recently I have been in need for software capable of statistical analysis doing one way analysis of variance (ANOVA). I need it to check how significant the differences are between gene-expression levels from each organ that were tested. Following ANOVA, a POST HOC analysis using Tukey HSD is also desirable, as it can provide more detailed data.

In my undergraduate years, I only had a short period of interaction with statistical analysis. The program that I used then was SPSS 9.0. In my home country, where the majority of the programs sold are pirated versions, they can be had for ridiculously cheap prices. With weak law enforcement and the inability to purchase, pirated software is the norm in many developing countries. I have just realized the damage of pirated copies on our morality after I went abroad.

Anyway, back to the topic, as I remembered, SPSS 9.0 was a very useful and easy to use program. If I am not mistaken, one way ANOVA is not really that complicated, and can be done manually, but I don’t have the time and patience to re-learn that subject again. Eventually I downloaded the most current SPSS release, SPSS 19. Fortunately, in 15 days after installation, it can be used in full function as a demo. And I was able to conduct ANOVA along with the POST HOC tests with no problem at all. However, the program will stop working after 15 days and needs to be purchased.

In the long run, I will definitely need a statistical analysis program. However, at around 1.000 USD, I assume that SPSS 19 is overkill for me. So I started to look for free alternatives. The first alternative that I bumped into is PSPP (, a very capable program, which is a clone of SPSS minus some bells and whistles. It’s easy to use, can perform ANOVA, but unfortunately, doesn’t have the ability to conduct POST HOC analysis.

So I searched for other programs on the internet. The ones that didn’t work out for me was SOFA (, assistat (, openstat (, and others. They may be able to do the job, but for me the interface was just too difficult, awkward, and most importantly, I failed achieve what I intended. Of course everyone is entitled to a different opinion, and might find those programs OK for their needs.

I finally stumbled upon brightstat ( It’s an online analysis suite which can perform ANOVA along with POST HOC analysis, exactly what I need for analysis of my data. The interface is user friendly and very intuitive. I performed the same analysis which I performed on SPSS 19 and it gave similar results. It even has the option of creating nice looking graphs as well.

SPSS 19 is no doubt a wonderful program for performing statistical analysis, especially due to the fact that it is widely used with abundance of references and tutorials online. However, if statistical analysis is not your main work and only need it as complimentary data, there are many free programs out there that might suite your needs. For me, brightstat coupled with PSPP is more than what I currently need (ANOVA with POST HOC analysis).

*POST HOC analysis: gives information on how significant the differences are between the mean values of each sample.


Anonymous said...

Wow, great set of resources, thanks. I teach stats to psych students, but always looking for alternatives to SPSS. Your article's got me trying a couple of them - I'd almost given up in despair after wading through obtuse instructions on using "R", with an entire command-line language to learn. So... thanks.

Fendrri said...

Your welcome. I think I also bumped into "R". But as you said, I also thought that the command line language will be a pain to learn. :)

Daniel Stricker said...

Brightstat is now redesigned and relaunched as a web-application. You can do statistics and data visualization on any desktop, handheld or mobile device. Check it out:

Daniel Stricker said...

Brightstat has been redesigned and relaunched as a web-application. You can do now statistical analyses and data visualization on any desktop, handheld or mobile device. Check it out: