Shannon Conners manages production of new JMP software releases within the research and development group of the JMP division of SAS. Before joining JMP in 2006 as JMP Genomics product manager, she used SAS and JMP to analyze and visualize microarray data from microbes from extreme environments during her PhD studies and postdoctoral work in bioinformatics at North Carolina State University.
For JMP Genomics 3.2, we had several requests from users to implement GCRMA background correction in our CEL import process. Similar to the request to implement RMA for JMP Genomics 3.0, this was primarily motivated by customers’ desire to process relatively large data sets without being limited by RAM memory.
JMP Genomics development group leader Russ Wolfinger and Padraic Neville (SAS Analytics R&D) recently attended the 8th Face-to-Face meeting of the MicroArray Quality Control (MAQC) Consortium at the FDA in Rockville, MD. Results of the first phase of MAQC were published in the journal Nature Biotechnology in late 2006 and
This blog post is the first of two that will describe new basic workflows in JMP Genomics 3.2. The basic workflows offer an intermediate step between the highly flexible Workflow Builder first introduced in JMP Genomics 3.0 and the simplicity of the streamlined Affymetrix Expression CHP Wizard, which first appeared
I’m glad to report that JMP Genomics 3.2 has been officially released as a Web update. The development and testing team has been working very hard on this release since last November when the JMP Genomics 3.1 update was posted. We are all breathing a little easier now with the
Again for JMP Genomics 3.2, I have to praise the efforts of our documentation specialist Tom Pedersen. He has spent many hours toiling away on chapters with lots of detail on nearly every JMP Genomics process. His job can really be a thankless one at times-chasing after developers (or a
I had an interesting conversation with a longtime JMP Genomics user the other day about open source vs. commercial software after (yet another) query from a prospect about what makes JMP Genomics different from free genomics software tools. This may be a controversial topic, and there are plenty who won’t
JMP Genomics and partners Affymetrix and Ingenuity Systems will be holding seminars in Malvern, PA (May 6), and Bridgewater, NJ (May 7). These seminars will cover many aspects of a complete expression analysis workflow, from the use of Affymetrix array platforms to generate expression data, to filtering, statistical and biological
Field application scientist Doug Robinson and JMP Account Executive Susan Glick recently attended an excellent conference on next-generation sequencing, organized by JMP Genomics customer National Center for Genome Resources. This conference, held March 6-7 in Santa Fe, NM, was sponsored by JMP Genomics, Illumina, and Roche, among others. JMP Genomics
We’ve had several customers who have been surprised that JMP Genomics can handle high-throughput data generated on non-array platforms. These customers and others are glad to hear that JMP Genomics can also handle TaqMan data, processed NextGen sequencing data, and data generated on custom array platforms or other commercial platforms
JMP Genomics 3.1 includes a new streamlined application for the analysis of Affymetrix CHP files, the Affymetrix Expression CHP Wizard. The wizard is designed to quickly introduce new users to a typical expression analysis workflow in JMP Genomics. This new tool uses an interactive interface to collect required information about