Sort trellised charts by P-value

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Sort trellised Land charts by P-value

Introduction

In certain Views within Land data, you can apply a trellis to subset the data across multiple charts by a selected metadata column. Once you have applied a trellis, you can change the ordering of the charts from "Sort by trellis covariate" (alphabetically by the covariate), to "sort by P-value". This enables you to quickly find the charts with data that were found to have significant differences between the data in the visible chart.

Step 1: Open a supported plot

Most charts that 1. Can be trellised by a covariate 2. Have "Show summary information" or "Change Regression Line Setting" (so can calculate a P-value) can be re-ordered by P-value. Examples include Gene FPKM, Comparison Correlation, Integration (Scan All Genes), and Survival plots.

Charts that are pre-trellised, such as the Gene FPKM (Project View) or Transcript FPKM (Individual Chart) cannot be changed.

For example, search for ERBB2 in OncoGEO, then select the Gene FPKM chart.

ERBB2 GeneFPKM.png

Step 2: trellis on a covariate

Select a useful metadata column to subset the data on. For example, if looking at disease-vs-normal expression across a variety of diseases, try trellising on TissueCategory. It's best to trellis on fewer than 50 charts, or the sorting in step 4 may take a while.

For example, trellis ERBB2 expression on TissueCategory, to see how ERBB2 expression differs across multiple disease and normal samples in each Tissue Category.

ERBB2 TrellisTissueCategory.png

Step 3: Display the P-value

Before sorting on P-value, be sure to display the P-value information.

In certain plots (Scatter plots such as Integration| Scan All Genes), under Customize, you will find "Change Regression Line Setting". Select "Line+Summary".

In other plots (Variable Views, Survival plots), click "Show Summary Information".

Step 4: Click "Sort on P-value"

Click "Sort on P-value" to re-order the data.

Tips.pngSome charts, like Gene FPKM, will only display a P-value if multiple profile columns are selected.


For example, change "Specify Multiple Profile Columns" to TissueCategory+DiseaseCategory,

ERBB2 ProfileTissueDisease.png

then sort on P-value.

Scroll down to explore the differences across diseases within each Tissue Category.

For example, two different Disease Categories from the same tissue may have very different expression:

ERBB2 Sorted.png

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