Process Description

Two-Way Plotter

The Two-Way Plotter draws line plots and bar charts in .html for selected rows of a tall data set and two selected experimental design variables in order to visualize the effects of individual experimental factors or to detect possible interactions between experimental factors for a given gene or set of genes. This process is typically run once a set of genes of interest have been identified, normally by ANOVA or some other analysis. Plots are constructed only for selected rows in the chosen data set, as specified by the value of a separate ID variable.

What do I need?

Two data sets are required for this process.

The first, the Input Data Set, contains all of the numeric data to be analyzed. For most cases, the use of normalized data, in which global effects, such as dye, chip to chip variation, and so on, have been removed, is recommended. This data set must be a tall data set.

The second data set is the Experimental Design Data Set (EDDS). This required data set tells how the experiment was performed, providing information about the columns in the input data set. Note that one column in the EDDS must be named ColumnName and the values contained in this column must exactly match the column names in the input data set.

An Annotation Data Set can also be specified. This data set contains information, such as gene identity, accession numbers, chromosomal location, and so on, for each of the rows in the input data set. This data set is also in the tall format, where each row corresponds to a different gene.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output generated by this process is summarized in .pdf file. Refer to the Two-Way Plotter output documentation for detailed descriptions.