Redundant siRNA Activity (RSA) Analysis
(Windows Release)
Probabilistic Hit Selection Algorithm

Download the installation .MSI file, run it on your Windows machine. The program will prompt you to install a free MS .NET Framkwork 3.5 package (from MicroSoft) first, if it is not already installed. Successful installation will create a program folder called "GNF" under your Start menu. Feel free to create a desktop shortcut afterwards.

Usage of Graphical Interface

Step 1. Click "Input" to choose an input file. The file must be in CSV format
      the spreadsheet must contain at least three columns:
        Gene_ID: the gene identifier for the well
        Well_ID: the well identifier
        Score: numerical value for hit picking
      Notice:
        1) the order of the these three columns can be arbitrary
        2) wells share the same Gene_ID are consider independent siRNAs for the same gene
        3) wells are ignored, if Gene_ID or Score is not defined

Step 2. Specify lower boundary and upper boundary.

      Check "Reverse" only if you are looking for high-score wells.

Step 3. Specify output file name, click "Run".

Usage of The Command Line Version

    Syntax: RSAConsole.exe [Options]
      -lb: lower_bound, defaults to 0
      -ub: upper bound, defaults to 1
      -isReverse: reverse hit picking, the higher the score the better
          if -isReverse flag is off, the lower the score the better
      -inputFN: input file name
      -outputFN: output file name
  
   
Command Line Examples
      RSAConsole.exe --lb 0.2 --ub 0.8 --inputFN="C:\input.csv" --outputFN="C:\output.csv"
        wells with lower scores are considered more active
        wells <=0.2 are guaranteed hits, wells >0.8 are guaranteed non-hits
        wells (0.2,0.8] are determined by RSA algorithm
        output results in output.csv file
  
      RSAConsole.exe --lb 1.5 --ub 2.0 --inputFN="C:\input.csv" --outputFN="C:\output.csv"
        wells with higher scores are considered more active (specified by -r flag)
        wells >=2.0 are guaranteed hits, wells <1.2 are guaranteed non-hits
        wells [1.2,2.0) are determined by RSA algorithm
        output results in output.csv file

Output Format

  Gene_ID,Well_ID,Score: columns from input spreadsheet
  LogP: RSA p-value in log10, i.e., -2 means 0.01;
  RSA_Hit: whether the well is a hit, 1 means yes, 0 means no;
  #hitWell: number of hit wells for the gene
  #totalWell: total number of wells for the gene
    if gene A has three wells w1, w2 and w3, and w1 and w2 are hits,
    #totalWell should be 3, #hitWell should be 2, w1 and w2 should have RSA_Hit set as 1
    and w3 should have RSA_Hit set as 0.
  OPI_Rank: ranking column to sort all wells for hit picking
  Cutoff_Rank: ranking column to sort all wells based on Score in the simple activity-based method

  Note: a rank value of 999999 means the well is not a hit. We put a large rank number here
  for the convenient of spreadsheet sorting.

  Examples A in output.csv:
  -------------------------
  1221200,7_O20,0.0541,-6.810,1,3,3,1,33
  1221200,18_A21,0.0626,-6.810,1,3,3,2,43
  1221200,41_A21,0.0765,-6.810,1,3,3,3,72

  Gene ID 1221200 has three wells, 7_O20, 18_A21 and 41_A21. All show good scores.
  Therefore 3 out of 3 wells are hits (#totalWell=3, #hitWell=3, RSA_Hit=1 for all three wells)
  LogP is -6.810. These three wells are ranked as the best three wells by RSA.
  However, they are ranked as the 33th, 43th and 73th well by the traditional cutoff method.

  Examples B in output.csv:
  -------------------------
  3620,21_I17,0.0537,-2.344,1,1,2,162,31
  3620,44_I17,0.7335,-2.344,0,1,2,999999,4113

  Gene ID 3620 has two wells, 21_I17 is active, while 44_I17 is relative inactive.
  RSA decides that only 1 out of the 2 wells is a hit. Therefore one well has RSA_Hit set as 1,
  and the other 0. #totalWell=2, but #hitWell=1.
  The first well is the 162th hit by RSA, 31th by cutoff method.
  The second well is not a hit by RSA, 4113th by cutoff method.

Credits

Bin Zhou, bzhou_at_gnf_dot_org & Yingyao Zhou, yzhou_at_gnf_dot_org, Oct 28, 2008