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