Chipster manual

## Manual for Chipster

Chipster is an analysis software for DNA microarray expression data. Most of the analysis tools have been implemented in R. We are also drawing on the ready-made annotation packages for commercially available chips. Currently Chipster works best with Affymetrix, Agilent and Illumina data. It is capable of importing also cDNA data, but since most of these do not have an annotation package in the Bioconductor repository, the functionality that requires annotation packages (for example annotation, pathway enrichment and and promoter analysis) is disabled.

- General

- General functionality of Chipster
- Supported microarray chip types
- Accepted data formats
- Software requirements

- Working with Chipster

- Data import and preprocessing
- Analysis tools
- Tutorials
- Outline of expression data analysis

- For developers
- Copyright

### Data import and preprocessing

Chipster is rather flexible in what type of data it can import. Data import and preprocessing have been described in more detail in these documents.

- Affymetrix
  - Import
  - Normalize
  - Analysis wizard
- Illumina
  - Import
  - Normalize
- Agilent (2-color)
  - Import
  - Normalize
- Agilent (1-color)
  - Import
  - Normalize
- cDNA
  - Import
  - Normalize
- Prenormalized data
  - Import

### Tools

Every tool is decribed in detail on its own help page. The help page is divided into four parts: General description, Parameters, Details on how the tool works, and Output where the results are described. The Parameters part contains the list of parameters, their possible values (1-100) and their default values [10].

- Annotation / Affymetrix gene list
- Clustering / Hierarchical
- Clustering / K-means
- Clustering / KNN classification
- Clustering / SOM
- Clustering / QT
- Normalisation / Affymetrix
- Normalisation / Affymetrix exon arrays
- Normalisation / Agilent 2-color
- Normalisation / Agilent 1-color
- Normalisation / cDNA
- Normalisation / Illumina - BeadStudio output
- Normalisation / random effects
- Pathways / Hypergeometric test for GO
- Pathways / Hypergeometric test for KEGG / PFAM
- Pathways / Gene set test
- Pathways / Bayesian network
- Pathways / Boolean network
- Preprocessing / Filter by CV
- Preprocessing / Filter by expression
- Preprocessing / Filter by flags
- Preprocessing / Filter by standard deviation
- Preprocessing / Filter by interquartile range
- Preprocessing / Impute missing values
- Preprocessing / Remove missing values
- Quality control / Affymetrix
- Quality control / Affymetrix RLE/NUSE
- Quality control / Agilent
- Quality control / Agilent 1-color
- Quality control / cDNA
- Quality control / Illumina
- Promoter analysis / Weeder
- Promoter analysis / ClusterBuster
- Promoter analysis / Retrieve promoters
- Statistics / One sample tests
- Statistics / NMDS
- Statistics / PCA
- Statistics / Several groups tests
- Statistics / Single-slide methods
- Statistics / Time series
- Statistics / Two groups tests
- Statistics / Correlate with phenodata
- Statistics / Sample size estimation
- Statistics / Linear modelling
- Utilities / Export tab2mage format
- Utilities / Export GEO's SOFT format
- Utilities / Import from GEO
- Utilities / Merge tables
- Utilities / Average replicates
- Utilities / Calculate descriptive statistics
- Utilities / Calculate fold change
- Utilities / Extract genes from clustering
- Utilities / Extract genes from a statistical test results
- Utilities / Extract samples from dataset
- Utilities / Generate phenodata
- Utilities / Search by correlation
- Utilities / Search by gene name
- Utilities / Filter by column
- Visualisation / Chromosomal position
- Visualisation / Idiogram
- Visualisation / Volcano plot
- Visualisation / Volcano plot from existing results
- Visualisation / Boxplot
- Visualisation / Correlogram
- Visualisation / Dendrogram
- Visualisation / Heatmap
- Visualisation / Histogram
- Visualisation / Venn-diagram

### For developers

Chipster is an open source software that will be available for downloading from Sourceforge. The Wiki in Sourceforge provides developers with extra information regarding a local installation and configuring and strating the system:

- Architecture description
- Server installation instructions
- Starting client without Java Webstart
- Generating your own SSL keys
- Installing required external software
- Adding new R scripts

### Copyright

- Copyright notice for Chipster
- Copyright notice for this manual