Table 1

Representative analysis methods held in the ArrayQuest Methods Library.

Method Title

Method Description

Required Data Format

Data Source

Programming Language/ Software¹

Output

RMA Normalization of Affymetrix Data

This method performs Robust Multichip Analysis (RMA) to generate normalized expression intensities for a set of Affymetrix GeneChip CEL files.

Affymetrix GeneChip data in .CEL file format

MUSC DNA Microarray Database or User's Private Database

R/Bioconductor

A Microsoft Excel file of normalized intensities transformed into log base 2 for all genes and four JPEG files of box plots and histograms of expression intensities before and after normalization.

Identification of differentially expressed genes based on fold-change, p-value and/or FDR parameters

This method is used to analyze data from any two-condition microarray experiment. The algorithm normalizes hybridization data, finds differentially expressed genes based on fold-change, t-test and FDR thresholds, collects annotations for these genes, performs hierarchical clustering and renders a heat map of the expression profiles.

Affymetrix GeneChip data in .CEL file format

MUSC DNA Microarray Database or User's Private Database

R/Bioconductor

Annotation reports (Excel and HTML); Heatmap of differentially expressed genes (.JPEG); KEGG pathway heat maps of differentially expressed genes (as many as are found) (.JPEG); GO Information (HTML).

Identification of differentially expressed genes based on p-value, fold-change and/or FDR parameters: .SOFT files only

This method is used to analyze Affymetrix DNA microarray data that can be obtained from NIH GEO as a .SOFT.gz file. The method normalizes hybridization data (RMA), finds differentially expressed genes based on fold-change, t-test and FDR thresholds, collects annotations for these genes, performs hierarchical clustering and renders a heat map of the expression profiles.

Affymetrix GeneChip data in GEO .SOFT file format

Gene Expression Omnibus (GEO)

R/Bioconductor

Annotation reports (Excel and HTML); Heatmap of differentially expressed genes (.JPEG); KEGG pathway heat maps of differentially expressed genes (as many as are found) (.JPEG); GO Information (HTML).

Assessment of gene expression associated with a specified GO ID(s)

This method analyzes Affymetrix GeneChip data to find gene expression values associated with specified GO IDs. The script normalizes GeneChip hybridization data (RMA), extracts hybridization values for genes associated with a user-provided GO ID, performs hierarchical clustering and renders a heat map of the expression profiles.

Affymetrix GeneChip data in .CEL file format

MUSC DNA Microarray Database or User's Private Database

R/Bioconductor

Boxplots and histograms of expression intensities before and after normalization (each in JPEG). Heat map based on the number of GO IDs provided by the user (each in JPEG).

¹ArrayQuest methods displayed in this table are written using the R statistical computing language [13] and implement packages/algorithms that are the product of the Bioconductor Open Source software development project [2]. Bioconductor packages used in ArrayQuest methods and links to package descriptions and developers are given in the description window for each method in the ArrayQuest Methods Library [11].

Argraves et al. BMC Bioinformatics 2005 6:287   doi:10.1186/1471-2105-6-287