JMP Genomics 5 released

Animation of the structure of a section of DNA...
Image via Wikipedia

Close to the launch of JMP9 with it’s R integration comes the announcement of JMP Genomics 5 released. The product brief is available here and it has an interesting mix of features. If you want to try out the features you can see

As per me, I snagged some “new”stuff in this release-

  • Perform enrichment analysis using functional information from Ingenuity Pathways Analysis.+
  • New bar chart track allows summarization of reads or intensities.
  • New color map track displays heat plots of information for individual subjects.
  • Use a variety of continuous measures for summarization.
  • Using a common identifier, compare list membership for up tofive groups and display overlaps with Venn diagrams.
  • Filter or shade segments by mean intensity, with an optionto display segment mean intensity and set a reference valuefor shading.
  • Adjust intensities or counts for experimental samples using paired or grouped control samples.
  • Screen paired DNA and RNA intensities for allele-specific expression.
  • Standardize using a shifting factor and perform log2transformation after standardization.
  • Use kernel density information in loess and quantile normalization.
  • Depict partition tree information graphically for standard models with new Tree Viewer
  • Predictive modeling for survival analysis with Harrell’s assessment method and integration with Cross-Validation Model Comparison.

That’s right- that is incorporating the work of our favorite professor from R Project himself-

Apparently Prof Frank E was quite a SAS coder himself (see

Back to JMP Genomics 5-

The JMP software platform provides:

• New integration capabilities let R users leverage JMP’s interactivegraphics to display analytic results.

• Tools for R programmers to build and package user interfaces that let them share customized R analytics with a broader audience.•

A new add-in infrastructure that simplifies the integration of external analytics into JMP.


+ For people in life sciences who like new stats software you can also download a trial version of IPA here at

John Sall sets JMP 9 free to tango with R


Diagnostic graphs produced by plot.lm() functi...
Image via Wikipedia


John Sall, founder SAS AND JMP , has released the latest blockbuster edition of flagship of JMP 9 (JMP Stands for John’s Macintosh Program).

To kill all birds with one software, it is integrated with R and SAS, and the brochure frankly lists all the qualities. Why am I excited for JMP 9 integration with R and with SAS- well it integrates bigger datasets manipulation (thanks to SAS) with R’s superb library of statistical packages and a great statistical GUI (JMP). This makes JMP the latest software apart from SAS/IML, Rapid Miner,Knime, Oracle Data Miner to showcase it’s R integration (without getting into the GPL compliance need for showing source code– it does not ship R- and advises you to just freely download R). I am sure Peter Dalgaard, and Frankie Harell are all overjoyed that R Base and Hmisc packages would be used by fellow statisticians  and students for JMP- which after all is made in the neighborhood state of North Carolina.

Best of all a JMP 30 day trial is free- so no money lost if you download JMP 9 (and no they dont ask for your credit card number, or do they- but they do have a huuuuuuge form to register before you download. Still JMP 9 the software itself is more thoughtfully designed than the email-prospect-leads-form and the extra functionality in the free 30 day trial is worth it.

Also see “New Features  in JMP 9

which has this regarding R.

Working with R

R is a programming language and software environment for statistical computing and graphics. JMP now  supports a set of JSL functions to access R. The JSL functions provide the following options:

• open and close a connection between JMP and R

• exchange data between JMP and R

•submit R code for execution

•display graphics produced by R

JMP and R each have their own sets of computational methods.

R has some methods that JMP does not have. Using JSL functions, you can connect to R and use these R computational methods from within JMP.

Textual output and error messages from R appear in the log window.R must be installed on the same computer as JMP.

JMP is not distributed with a copy of R. You can download R from the Comprehensive R Archive Network Web site:

Because JMP is supported as both a 32-bit and a 64-bit Windows application, you must install the corresponding 32-bit or 64-bit version of R.

For details, see the Scripting Guide book.

and the download trial page ( search optimized URL) –

In related news (Richest man in North Carolina also ranks nationally( , Jim Goodnight is now just as rich as Mark Zuckenberg, creator of Facebook-

though probably they are not creating a movie on Jim yet (imagine a movie titled “The Statistical Software” -not just the same dude feel as “The Social Network”)

See John’s latest interview :

The People Behind the Software: John Sall

Interview John Sall Founder JMP/SAS Institute

SAS Early Days

JMP 9 releasing on Oct 12

JMP 9 releases on Oct 12- it is a very good reliable data visualization and analytical tool ( AND available on Mac as well)

AND IT is advertising R Graphics as well (lol- I can visualize the look on some ahem SAS fans in the R Project)

Updated Pricing- note I am not sure why they are charging US academics 495$ when SAS On Demand is free for academics. Shouldnt JMP be free to students- maybe John Sall and his people can do a tradeoff analysis for this given JMP’s graphics are better than Base SAS (which is under some pressure from WPS and R)


*Offer good in the U.S. only.

New Corporate Customer


Save $300.

No special requirements.
Corporate Upgrade


Save $155.

Complete the form below or call 1-877-594-6567. Requires valid JMP® 8 serial number.
New Academic


Save $100.

Complete the form below or call 1-877-594-6567. Requires campus street address and campus e-mail address.
Academic Upgrade


Save $45.

Complete the form below or call 1-877-594-6567. Requires campus street address and campus e-mail address.

From- the mailer-

Be First in Line for JMP® 9
Save up to $300 when you pre-order a
single-user license by Oct. 11

Pre-Order JMP 9

Make JMP your analytic hub for visual data discovery with this special offer, good through Oct. 11, 2010. Pre-order a single-user license of JMP 9 – for a discount of up to $300 – and get ready for a leap in data interactivity.

Order now and enjoy the compelling new features of JMP 9 when the software is released Oct. 12. New capabilities in JMP 9 let you:

  • Optimize and simulate using your Microsoft Excel spreadsheets.
  • Use maps to find patterns in your geographic data.
  • Enjoy the updated look and flexibility of JMP 9 on Microsoft Windows.
  • Create and share custom add-ins that extend JMP.
  • Leverage an expanded array of advanced statistical methodologies.
  • Display analytic results from R using interactive graphics.


What if I already have a JMP 8 single-user license?
Great news! You can upgrade to JMP 9 for less than half the regular price.

What if I’m an annual license customer?
Don’t worry, we’ve got you covered. Annual license customers enjoy priority access to all the latest JMP releases as soon as they become available. JMP 9 will be shipped to you automatically.

What if I work or study in the academic world?
Call 1-877-594-6567 to learn about significant discounts for students and professors through the JMP Academic Program.

Please feel free to forward this offer to interested colleagues.

Got two or more users?
A JMP® annual license is the way to go. Call for details.

Remember: Act by Oct. 11!

JMP runs on Macintosh and Windows