From: ArrayQuest: a web resource for the analysis of DNA microarray data
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). |