Dynamically Choose Housekeepers

Number of Housekeepers Auto-Select

"Auto-select" utilizes geNorm to identify the optimal number of housekeepers.

Dynamically Choose Housekeepers
Uses the geNorm algorithm (Vandesompele et al., Genome Biology, 2002) to identify the most stably expressed genes up to the number specified from among the annotated housekeepers and normalizes the data using these genes. This option is recommended for use with raw data. Selection of this option with normalized data will override normalization performed in the experiment wizard.

Run QC and Descriptive Analyses

Run QC and Descriptive Analyses
Selection of this option generates descriptive plots, including heatmaps and principal component analysis of the whole dataset and of smaller gene sets, and summaries of experimental variables' distribution and association with gene expression. This option is recommended for all analyses.

Threshold Low Count Data

Threshold Count Value Observation Frequency

Threshold Low Count Data
Removes genes from the analysis based on a specified threshold count value and observation frequency across all samples. Genes that fall below the threshold at a frequency greater than the specified observation frequency will be removed from the analysis.

Threshold count value: (min = 0, max = 100)
Observation frequency: (min = 0, max = 1)

Choose Additional Image Types to Create

Additional Image Types
Select optional additional image output format - .png files will be created automatically

Annotation Defining Gene Sets
Use Default (Immune.Response.Category)
Custom

Column Defining Gene Sets
Choose annotation information for all gene set analyses. By default, gene sets will be annotated using information defined in the Immune Response Category column.