Chipster user friendly analysis tool for microarray data

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Chipster user friendly analysis tool for
microarray data

• Eija Korpelainen
• Center for Scientific Computing, Finland
• eija.korpelainen_at_csc.fi

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Chipster

• Goal Easy access to up-to-date analysis methods
  (R/Bioconductor)
• Features
• Easy to use graphical interface
• Comprehensive selection of analysis tools and
  visualizations
• Support for different array types (Affymetrix,
  Agilent, Illumina, cDNA)
• Possibility to construct (and share) analysis
  workflows
• Compatible with Windows, Linux and Mac OS X
• Easy to install and update
• Graphical client program on users computer sends
  analysis jobs to central computing servers
• Availability
• Guest accounts for evaluation
• Open source (http//chipster.sourceforge.net)
• http//chipster.csc.fi

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• Aleksi Kallio
• Jarno Tuimala
• Taavi Hupponen
• Petri Klemelä, Mikko Koski, Janne Käki, Mika
  Rissanen
• All the pilot users
• Department of Computer Science, University of
  Helsinki
• Tekes, the Finnish Funding Agency for Technology
  and Innovation

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• Affymetrix HG-U133A dataset of 17 samples by
  Lenburg et al (GEO GDS505) Comparison of renal
  clear cell tumor tissue and adjacent normal
  tissue
• Finding differentially expressed genes and
  analyzing them (annotations, pathways, promoters)
• Visualizations
• Saving the analysis workflow for re-use

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Analysis tool content

• In addition to the usual analysis content such as
  normalization, filtering, statistics, clustering
  and annotations, Chipster provides
• Quality control methods
• Linear (mixed) models
• Bootstrapping of hierarchical clustering results
• Alternative mappings of the Affymetrix arrays
  (altCDF)
• Gene set enrichment analysis
• Promoter analysis

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Visualizing the data

• Interactive visualizations produced by the client
  program
• Histogram
• 2D and 3D scatterplot
• Expression profiles
• Clustered profiles
• Hierarchical clustering
• SOM clustering
• Static images produced by R/Bioconductor
• Volcano plot
• Box plot
• Heatmap
• Venn diagram
• Idiogram
• Chromosomal position
• Correlogram
• Dendrogram
• QC stats plot
• Ordination plots (NMDS, PCA)

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Automatic tracking of analysis history
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Workflow reusing your analysis pipeline

• Creates a macro that can be applied to another
  normalized dataset and phenodata
• Choose a dataset, and workflow records the
  analysis steps starting from it
• You can change parameters directly to the
  workflow file (e.g. affymetrix.bsh) located in
  the chipster-scripts folder
• Workflows can be shared with other users

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Wizard for Affymetrix data

• Ready-made workflow to find differentially
  expressed genes
• Normalization
• Phenodata creation
• Statistical test
• Hierarchical clustering