dChip: User’s Manual

(More pages at User group, including * links)

Data processing

Introduction, installation and user support *                           Prepare data, file format and example method description

Gene information file, make or classify gene list                   Read in CEL and CDF files, sample information file                                  

Read external data file                                                            Combine data from different array types or species 

Automated analysis *                                                             Interface with R software *

Designing experiments                                                                                                 

Probe-level analysis

Normalize arrays                                                                     View array image, export image and CEL file

View and export PM/MM probe data                                      Compute and export model-based expression value, outlier array

Exon and tiling array analysis *

High-level analysis

Array list file, handle batch effect                                          Filter genes

Compare samples                                                                    Hierarchical clustering                                                                                

Gene function enrichment analysis                                         Time course and correlation analysis, Analysis of Variance                             

Map genes to chromosome                                                      Sample classification by LDA, PCA

SNP array analysis

SNP array data processing                                                      View expression, SNP, CGH data along chromosome

LOH and copy number analysis                                              Chromosome regions, clustering using SNP data

Parametric linkage analysis                                                     Allele sharing analysis                                                                                   

Compute and permute summary score

 

Manual in PDF: Oct. 2005, Oct. 2002                                     References and acknowledgments