dChip: User’s Manual

 

Data processing

Introduction, installation and user forum                                  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                         

Designing experiments                                                             Interface with R software                  

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