The Clough Lab
The Clough Lab







cDNA Summary Table
PROCEDURE PROGRAMS INPUT FILES OUTPUT FILES COMMENTS
1. Merge data and generate files for analysis merge_imputeblank1.pl
  • All .gpr files in the same folder and sorted according to the design file
  • Library array layout file
    •
  • Rinput.txt
  • flag_data.txt
  • Summary_flags.txt
  • rawdata_beforeBackground correction.txt
  • rawdata_beforeBackground correction_noblank.txt
    •
  • Input file for next step (normalization)
  • Input file for the 3rd step (clean data to create SAS input)
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    2. Transform and normalize data
  • Log tranformation (createData statement)
  • Normalization (transform.madata statement)

    • (Using R/maanova code)
  • Rinput.txt
  • DesignFile.txt
    •
  • PlotRawData.ps
  • PlotGLOWESS.ps
  • Normal_Data.csv
    •
  • Ratio intensity plots before normalization
  • Ratio intensity plots after normalization
  • Input file for next step in .txt format (clean data to create SAS input)
    •
    3. Remove bad spots and format for SAS changeflagand badspot.pl
  • flag_data.txt
  • Normal_Data.txt
    •
  • forsasinput.txt
  • replicatesforeachgene.txt
  • summary.txt (Under construction)
    •
  • Input file for next step and SAS analysis (convert to .csv format)
  • Input file for SAS analysis (convert to .csv format)
    •
    4. Calculate average intensity values calculatingAverageIntensity.pl
  • DesignFile.txt
  • forsasinput.txt
    •
  • AveIntensityOutput.txt
    •
  • Average intensity values of every gene for every sample
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    5. Statistics ANOVA SAS-ANOVA analysis
  • forsasinput.csv
  • replicatesforeachgene.csv
  • DesignFile.csv
    •
  • F-test output
  • Residual normality plot
  • List of significnat gens for each comparison done with replicates information (cutoff p_value=0.05)
    •
  • Need to change directory for input data
  • Need to change variable input statements according to number of arrays
  • Need to change ANOVA linear model according to experimental design
    •




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    This page last updated: November 30, 2005
    Designed by: Marisol Benitez, Jason Bant, Bob Trieu, Priya Pradhan anf Toyin Olagunju