The analysis of data obtained from microarray assays is an often problematic and tedious task. The reasons for the difficulty in analyzing microarray data is due primarily to the large amount of information the microarray format provides. Other obstacles include removal of erronious data points, sorting between samples and standards, as well as the difficulties of standardizing data. Several software packages are available and I am currently using the ArrayVision Version 8.0 to perform all my data analysis of protein microarrays. After sampling several software packages, I felt the ArrayVision 8.0 software was the best for several reasons including a large number of desirable and flexibile features, ease of use, quality of data outputs/reports and of course, price.
Overall, the software is fairly straightforward and the initial user interface is simple and understandable. The software is slightly complex in function, taking about two days of use to really get up to speed. However, considering the power of software, I think it is well-designed and intuitive, despite the time required by users to familiarize themselves with the software. The screens, hot-buttons and menus are grouped by function and are easy to understand and navigate.
The ArrayVision software can be used to analyze arrays with fluorescent, radio-isotopic and chemiluminescent content with specific analysis protocol templates for each type. The analysis wizard in the software is particularly useful when designing the analysis parameters. There is a specific analysis template for the fluorescent, radio-isotopic and chemiluminescent signal array types with sub-types of expression, comparative expression, screening and protein analysis available for each signal type. These templates differ in data labeling, data sorting and final analysis reports and are designed such that you can obtain the information you need.
The user first creates the protocol which will be used in the analysis wizard. Initially, adjusting the protocol templates to your array layouts is slightly difficult. However, after creating a few templates the process becomes more intuitive and the software very flexible to use. I especially liked the inputs for the array layout patterns, which are much more flexible and easier to use than most other software packages I have used. Once the protocol editor has been used to create an array wizard template, it may be saved and subsequent analyses using the same layout are quite easy.
The array wizard template also enables the user to analyze large numbers of arrays very quickly, making the software useful for high throughput/high capacity users. Other general software features that make this package more favorable are the automatic spot/array alignment, spot segmentation and automated analysis. The visuals are also excellent, offering several spectrum types to view data as well as an excellent contrast adjustment system. Scatter plots and calibration curves which can be automatically created upon analysis are also in a useful format, displaying the data you need. Data such as formulas for deriving line equations, y-intercepts, R2 values and extrapolated concentrations from standard curves are all displayed in a useful manner. Background subtraction, scatter plots and standard curves can also be calculated using several different methods, an option that I have found excessively complex or unavailable in other software packages.
Regarding data analysis, ArrayVision offers a very comprehensive variety of data readouts and reports. The layouts of the data reports can be arranged by specificity, rows/columns, target and several others, depending on your selected template style. Additionally, a wide variety of data can be reported such as area, standard deviations, background subtracted values, position and many others.
My primary use for this software has been for multiplexed protein analysis and expression. When analyzing normal or abnormal human serum or plasma samples, the software seems to generate efficient standard curves and the data readouts are useful and clear. When running large numbers of test samples, I have found the software is efficient and fast.
Overall, this software package is excellent in its flexibility. I found it will generate large amounts of data in a very useful and practical manner, while still being fairly easy to use. Although expensive, I feel it is worth its price. Issues with technical service from GE Healthcare (obtaining or transferring licenses) were taken care of on the same day and in some cases within hours. I would suggest this software for any lab that needs a powerful and flexible data analysis tool for either laboratory research or large capacity, high throughput work.