Bioin401 Project: Microarray Pipeline

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Bioin401 Project Microarray Pipeline

• Chunyan Meng,
• Yifeng Liu,
• Chelsea Ju
• February 27, 2006

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Microarray Pipeline Background Synopsis

• Input Data Processing
• Normalization, Background correction
• Expression index calculation, Gene selection
• Data Interpretation
• Clustering
• Gene Annotation
• Gene Function Prediction
• Report Publisher
• Participants
• Yifeng Liu
• Chelsea Ju

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Microarray Pipeline GANTT Chart
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Microarray Pipeline Flow Chart
NormailzationYifeng
Server SetupChunyan
Statistical AnalysisYifeng
Web InterfaceGroup
ClusteringChunyan
AnnotationChelsea
PredictionChunyan
GenerateReportsChelsea Yifeng
DesignDocumetationGroup
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Micorarry PipelineRSPerl Problem and server

• Tried to figure out the problem of Calling RSPerl
  by system user. Couldnt succeed. So use system
  call to run R from perl.
• Configured the server so that apache can write
  data to the server properly by changing the owner
  of the cgi script to apache.
• The server is running OK after increased memory.

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Micorarry PipelineCEL file upload
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Micorarry PipelineCEL file upload
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Clustering Web Form
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Hiearchical Clustering (stats package)

• 7 methods for computing the between cluster
  distances

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Hiearchical Clustering (stats package)

• 6 distance measures for distance matrix
  computation

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Microarray Pipeline Dendrogram of average
linkage
Notes this is how the dendrogram will look like.
Generated by a R script which is not linked to
the web form yet.
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Microarray PipelineHeatmap with dendrogram
Yellow-Green-Blue sequential
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Microarray PipelineWhat to do next

• Link the R-script for Hierarchical Clustering
  with the web form.
• K-means Clustering Methods (R script)Available
  algorithms Hartigan-Wong, Lioyd, Forgy,
  MacQueen.
• Integrating different parts together.
• Check if protFunc (genepublisher used that) can
  be used for Gene Function Prediction.

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Microarray Pipeline GANTT Chart
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