VSN International / Newsletters / Vision No. 15 September 2009

Vision No. 15 September 2009

GenStat 12th edition available, now including QTL menus.

The latest version of GenStat, the pioneering data analysis tool for bioscientists, is now available for download. This latest edition has been updated and enhanced to include a host of new and improved statistical techniques of particular use and interest to plant breeders and scientists working in genetic research.

Specific new features include the addition of stability co-efficients and genotype + genotype-by- environment biplots for use in variety trials, quantile regression and a suite of menus for QTL analysis. Enhancements to the GenStat graphics features include facilities to allow interactive selection between plotting components, which will assist with the interpretation of data – see the Technical Tip below for more details. GenStat’s existing core areas such as regression, REML and multivariate analysis have also been enhanced ensuring GenStat’s statistical techniques remain relevant, reliable and current.

“GenStat 12 is an outstanding achievement in terms of statistical capability,” says Stewart Andrews, CEO, VSNi, “and, importantly, demonstrates VSNi’s appreciation of the need to assist with solving the issues we all face. In an era of climate change, food shortages and food security, we have upgraded GenStat with statistical routines needed by scientists working to solve problems in world agriculture today.”

“One of the guiding principles behind GenStat’s development from its conception has always been careful consideration for scientific validity,” says Professor Roger Payne, CTO, VSNi, “GenStat’s history and pedigree provides users with the security of knowing that the results from GenStat analysis are founded on sound statistical principles. GenStat’s intelligent and well-planned menu system and comprehensive suite of diagnostic messages work together to guide users to the most correct and appropriate analyses for their data. In short, you can use GenStat with complete confidence.”

Also new in the 12th Edition is an interface to CycDesigN, the package for computer generation of experimental designs which constructs optimal or near-optimal block and row-column designs, via the GenStat menus. CycDesigN has been developed for scientists and researchers conducting experiments in field, glasshouse or laboratory trials, incorporating the latest research developments in experimental design. To obtain the CycDesign interface download the relevant files from the VSNI website, or for more information on CycDesign go to the CycDesign website.

For more details on GenStat, including a full list of new features and capabilities look at the VSNi website.

Technical tip – Interactive graphics in GenStat 12

Amongst the myriad of new features for the 12th Edition of GenStat, one of the more exciting is the ability to use the graphics interactively by making use of the ‘HOT’ components within the command DGRAPH, which allow the user to start with a basic plot and add elements to aid interpretation.

For example, the graph below shows a canonical variates biplot (figure 1) which makes use of another new feature for the 12th Release, the ability to plot oblique axes (see the command AXIS for further details).

CVA chart















Of the four groups here, we may be interested in plotting some extra features around one, or more, of the groups. For this, a hotmenu can be created and displayed in the Graphics toolbar giving you a drop-down menu of extra features that can be plotted (figure 2).

Selecting plots image (fig2)








For this example we have several options, namely plotting the convex hulls or group means. If we select ‘Convex hull West’, ‘Group mean North’ and ‘Group mean South’ they will be added to the existing plot, as seen below. (figure 3)

CVA chart 2















Another element of the ‘hot’ components is the ability to select a point and plot extra information about that point. For this, we would use the hotdefinition parameter of DGRAPH. Selecting Hotchoice mode (the, new, rightmost button in the Graphics toolbar) (figure 4) allows us to select any hotpoints.

The new hot component button




In the example we selected points 1 and 22 and we can now see the orthogonal projections from those points onto the four oblique axes. (figure 5)

CVA chart 3















More information about the ‘hot’ components can be found in the help for DGRAPH.


Latest training courses

On 15th September we’ll be running a course on REML and multi-level models in GenStat. The course is designed to introduce the user to REML in GenStat, and provide the underlying knowledge and confidence to use it correctly and effectively. It highlights how the REML menus guide the user through very complicated analysis and explains the REML commands so that users can program any non-standard analyses.

The course covers 4 main sessions:

  • Analysis of variance
  • Meta analysis
  • Spatial analysis
  • Repeated measurements

For more details on both courses and to book email support or go to the training pages on our website.

Out and about with VSNi


From 22-25th September Stewart Andrews (CEO) and Carey Biggs (Commercial Director) will be in Bangkok at the ABIC Conference 2009.

From 27th September to 2nd October we are back in Australia at the Barossa Valley for the Association for the Advancement of Animal Breeding and Genetics Conference.

Professor Roger Payne, our Chief Technical Officer is speaking at the ASA-CSSA-SSSA, in Pittsburgh between 1st and 5th November.

If you would like to meet with VSNi staff at one of these events please email Carey Biggs to arrange the details.

We’re always updating the list of events we can support and sponsor – so please send us details of any events you are organising or involved in, and as we decide on more events for the future we’ll list them on our website.

Discussion

Comments are disallowed for this post.

Comments are closed.