Comparison.Table

From Array Suite Wiki

Jump to: navigation, search

Contents

Land Comparison Table

Overview

This Land View displays the full inference report for the selected pre-computed Land comparisons.

This View is available when one or more comparisons have been searched.

Comparison Table Contents

Each row will include information for one tested gene.

LandIPAButton.png

For each test (comparison), three columns will be included:

  • Log2 Fold Change: Fold-change values, as calculated by the test used, and log2-transformed
  • Raw PValue: Unadjusted P-value for this gene
  • Adjusted PValue: P-value, after adjusting for multiple tests (using Benjamini-Hochberg FDR)

Missing genes

All tested genes are included in this table. Depending on the platform and statistical test performed, certain genes may not be included.

For example, microarrays generally do not include all genes, so missing genes will not be reported.

Comparisons generated by DESeq2 for RNA-seq data will not include genes with no counts; flagged outliers will be included, but will not have P-values, and genes flagged by "independent filtering" will not include adjusted P-values.

[back to top]

Inference Table Manipulations

Table results can be filtered, sorted, exported, or sent to Ingenuity Pathway Analysis, by clicking the blue IPA button in the task bar.

Selecting a gene in the Comparison Table will select this gene in other Views, such as the Comparison Plot.

Use Find/Replace to find a gene of interest:

FindReplaceButton.png

FindMMP11.png

Then select this gene in the Comparison Table:

SelectMMP11.png

Switch to the Comparison Plot; the selected gene(s) will be selected (in plots where the gene was displayed).

VolcanoPlot MMP11.png

[back to top]

Related Articles

EnvelopeLarge2.png