JMPer Cable

Latest Posts

• Cross Evaluation and Progeny Simulation with JMP Genomics, Part 3: Cross Evaluation, Selection, and Progeny Simulation

  The Cross Evaluation tool in JMP Genomics allows for the evaluation of potential crosses using genetic markers and scoring code files. A scoring code is a SAS file containing a predictive model which quantifies the effects of numerous markers on a trait of interest. The scoring code files used in this example were created in last week’s post, Cross Evaluation and Progeny Simulation with JMP Genomi...

  Daniel_Genung

  JMPer Cable |

  Sep 5, 2019 12:47 PM

  3887 views | 0 replies
  

• Cross Evaluation and Progeny Simulation with JMP Genomics, Part 1: BLUP for Breeding Trial Data

  For this example, we have a set of 309 barley lines, which have been genotyped for ~3,500 markers each. We also have a set of measurements of four phenotypes taken from field trials from two separate locations over a two-year period. The phenotypes measured are protein content, test weight, ergosterol content, and protein yield. Before evaluating crosses and simulating progeny, we must capture the...

  Daniel_Genung

  JMPer Cable |

  Aug 28, 2019 9:36 AM

  7634 views | 0 replies
  

• Cross Evaluation and Progeny Simulation with JMP Genomics, Part 2: Predictive Modeling for Breeding Values

  In last week’s post, we consolidated breeding trial data into a single table using Best Linear Unbiased Prediction. The table below shows ~300 barley lines with phenotypic values for four traits and ~7000 genetic markers. In this post, we will use the Predictive Modeling Review tool in JMP Genomics to create multiple models and compare them via cross validation. After cross validation, we will sel...

  Daniel_Genung

  JMPer Cable |

  Aug 28, 2019 9:35 AM

  6087 views | 0 replies
  

• Navigating your reports using XPath

  Another way to navigate JMP reports? Yes, please!

  Wendy_Murphrey

  JMPer Cable |

  Aug 7, 2019 11:51 AM

  6982 views | 3 replies
  

• Using dates, times, datetimes and durations in JMP

  There are four common time-based values that you might have to deal with in JMP: dates, times, datetimes and durations.

  Jeff_Perkinson

  JMPer Cable |

  Jul 30, 2019 12:55 PM

  47339 views | 0 replies
  

• Posting to JMP Public

  Starting with JMP 14.2, JMP users will be able to publish their reports to JMP Public. Prepare your reports in JMP and publish them to JMP Public for others to view — even those who may not have JMP. 

  Owen_Fitzgerald

  JMPer Cable |

  Jul 30, 2019 9:57 AM

  5778 views | 0 replies
  

• Expression Analysis with JMP Genomics, Part 3: Basic Expression Workflow

  JMP Genomics has analytical pipelines or Workflows to perform a series of analyses on a data set. The Basic Expression Workflow automates a series of quality control and normalization methods, followed by ANOVA, to perform a basic expression analysis. For this workflow, we will inspect data from an experiment in which MCF7 cells, cells which cause tumors, are exposed to estrogen at three different...

  Daniel_Genung

  JMPer Cable |

  Jul 16, 2019 8:56 AM

  6379 views | 2 replies
  

• How to embed JMP Public or JMP Live content in a webpage or blog post

  I wanted to make several graphs in the articles interactive. I knew I could create the interactive graphics in JMP and move them to JMP Public. But I didn't know how to do the bit where I embed the JMP Public content in the article. So, here is how to do it.

  MikeD_Anderson

  JMPer Cable |

  Jul 12, 2019 8:04 AM

  7998 views | 4 replies
  

• Expression Analysis with JMP Genomics, Part 1: Experimental Design

  To perform expression analysis in JMP Genomics, an Experimental Design File (EDF) is required.  The EDF contains sample annotation information and/or phenotype information for a related expression data set. There are a few different ways to create this file but the best method for creating an EDF is dependent upon how your data is organized. For this guide, we create an EDF for a series of data fi...

  Daniel_Genung

  JMPer Cable |

  Jul 11, 2019 3:21 PM

  5075 views | 0 replies
  

• Expression Analysis with JMP Genomics, Part 2: Importing Expression Data from Text Files

  In last week’s blog post, we created an Experimental Design File (EDF) using JMP Genomics for a set of gene expression files corresponding to 18 different experimental groups. Now that the experimental design is organized into a SAS data set, the data files (in txt format) can be imported and concatenated into a single table using the Import a Designed Experiment from Text, CSV, or Excel Files too...

  Daniel_Genung

  JMPer Cable |

  Jul 5, 2019 12:03 PM

  4501 views | 0 replies
  

• 如何運用JMP進行可靠度(Reliability)分析

  合理應用可靠度分析，可以幫助研發、工程、品質等部門的技術人員提高產品品質的穩定性，降低產品全壽命週期費用和售後服務成本，改善顧客的滿意度和忠誠度。

  Ritalv

  JMPer Cable |

  Jul 2, 2019 6:44 PM

  6273 views | 0 replies
  

• Expression Analysis with JMP Genomics

  JMP Genomics is a specialized yet broad tool for analyzing genetic, genomic and other “-omic” data. Whether it's expression analysis, GWAS, predictive modeling, or plant breeding, JMP Genomics has a tool to meet the need.

  Daniel_Genung

  JMPer Cable |

  Jul 2, 2019 2:09 PM

  4711 views | 2 replies
  

• Genetic Association with JMP Genomics

  JMP Genomics is a specialized yet broad tool for analyzing genetic, genomic and other “-omic” data. Whether it's expression analysis, GWAS, predictive modeling, or plant breeding, JMP Genomics has a tool to meet the need. This blog series (the first in a set of four series) will handle genetic association beginning with the data import and continuing through several analytical pipelines.

  Daniel_Genung

  JMPer Cable |

  Jun 26, 2019 7:50 AM

  7022 views | 0 replies
  

• Genetic Association with JMP Genomics, Part 6: SNP-Trait Association

  JMP Genomics has an array of tools to associate genetic variants with traits. One of the most straightforward of these tools is SNP-Trait Association. By performing this analysis, you can quickly identify significant markers for multiple categorical or quantifiable traits. In this example, we explore ~22,000 markers for histiocytic sarcomas (tumors) in a sample of 474 Bernese Mountain Dogs. The ph...

  Daniel_Genung

  JMPer Cable |

  Jun 24, 2019 2:17 PM

  7779 views | 10 replies
  

• Genetic Association with JMP Genomics, Part 5: QTL Single Marker Analysis

  The QTL Single Marker Analysis tool in JMP Genomics performs a simple regression to correlate quantitative traits with markers within a genome. This tool is a great way to scan an entire set of markers and quickly identify loci of interest for a trait. In this example we will analyze 90 recombinant inbred lines of oat for their mean differential scanning calorimetry (DSC). Note that the two data s...

  Daniel_Genung

  JMPer Cable |

  Jun 18, 2019 1:42 PM

  4799 views | 0 replies
  

• Genetic Association with JMP Genomics, Part 4: Basic Linkage Mapping

  The Basic Linkage Mapping Workflow in JMP Genomics creates linkage maps using genetic marker data. The workflow includes output from the Recombination and Linkage Groups, Linkage Map Order, and Linkage Map Viewer. This includes calculation of recombination frequencies, testing for segregation distortion, assigning linkage groups to sets of markers, generating visualized linkage maps, and reorderin...

  Daniel_Genung

  JMPer Cable |

  Jun 18, 2019 1:01 PM

  4884 views | 0 replies
  

• Saving graphs, tables and reports in JMP

  Saving and sharing your output from JMP is easy. Here are some simple ways to save both tabular output and/or graphs in JMP.

  MaryLoveless

  JMPer Cable |

  Jun 14, 2019 5:41 AM

  91084 views | 19 replies
  

• How to make Harvey Balls in JMP in 3 ways

  OK, let's get something out of the way right from the start. There are so many jokes... so very many jokes... that I could make about this topic. But, I'm not going to make them. I'm going to take the high road. Not because I want to, if you've read any of my other articles, you'll know I revel in wordplay and corny jokes. No, I'm going to take the high road because I'm reasonably sure my editors ...

  MikeD_Anderson

  JMPer Cable |

  Jun 13, 2019 12:04 PM

  8349 views | 1 replies
  

• Genetic Association with JMP Genomics, Part 1: Importing and Cleaning Data

  In the Genetic Association with JMP Genomics series, we will discover numerous methods for associating genetic markers with traits of interest. Before starting any analyses, we need to import and clean our data. In this guide, we download a data set from GEO, bring it into JMP, and transform it into an ideal form for analysis. In this example, we explore ~22,000 genetic markers in a sample of 474 ...

  Daniel_Genung

  JMPer Cable |

  Jun 13, 2019 7:54 AM

  4753 views | 2 replies
  

• Genetic Association with JMP Genomics, Part 2: Basic Genetics Workflow (Case-Control)

  JMP Genomics has analytical pipelines or Workflows to perform a series of analyses on a data set. The Basic Genetics Workflow is a quick and easy method for gaining a deeper understanding of your data before beginning a more in-depth analysis. This workflow recodes marker data to a numeric format, imputes missing genotypic data, and creates data subsets based on minor allele frequency (MAF), missi...

  Daniel_Genung

  JMPer Cable |

  Jun 12, 2019 9:24 AM

  5110 views | 0 replies