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 timepoints. These cells reproduce rapidly when exposed to estrogen, and expression levels are expected to rise with continued exposure. This series of analyses will give a distribution of data at each timepoint under both control and experimental conditions, compare expression levels for each, and create a standardized data set for use with further analytical tools.
The Basic Expression Workflow is an effective way to string together a series of analyses and compare expression levels across experimental conditions. This workflow is highly recommended for launching into expression analysis. It allows for data standardization and QC, data exploration such as distribution and correlation analyses, and expression and LSMeans analysis. From the output window, it is easy to continue analysis in the Drill Downs menu and fit a model to your data.
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