comparison normalize.xml @ 10:0c4dcd3980c1 draft default tip

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9:600872152be6

<tool id="matrix_normalize" name="Matrix Normalize" version="1.0.0">
  <description>Matrix Normalize</description>
  <command interpreter="Rscript">normalize.r $genomicMatrix $normType $normBy 
#if str($controlColumnLabelsList) != "None":
    $controlColumnLabelsList 
#end if  

5. Normal normalization: same as exponential normalization, but inverse quantile function of Normal distribution is applied.

6. Weibull normalizations: same as exponential normalization, but inverse quantile function of Weibull distribution is applied with appropriate scale and shape parameters.


Normals parameter is an optional parameter which contains a list of column headers from the input matrix which should be considered as normals

  </help>   
</tool>

10:0c4dcd3980c1

<tool id="matrix_normalize" name="Matrix Normalize" version="2.0.0">
  <description>Matrix Normalize</description>
  <command interpreter="Rscript">normalize.r $genomicMatrix $normType $normBy 
#if str($controlColumnLabelsList) != "None":
    $controlColumnLabelsList 
#end if  

5. Normal normalization: same as exponential normalization, but inverse quantile function of Normal distribution is applied.

6. Weibull normalizations: same as exponential normalization, but inverse quantile function of Weibull distribution is applied with appropriate scale and shape parameters.


Normals/controls parameter is an optional parameter which contains either a list of column headers from the input matrix which should be considered as normals/controls, or a matrix of normal/control samples. The program is smart enough to distinguish between the two cases and will automatically process the normals/controls in a correct way. When specifying both the main expression matrix and the normals/controls matrix while performing column-wise normalization, the program will actually concatenate the two matrices and produce a combined matrix which contains both tumor and normal/control samples, in which samples are normalized.

  </help>   
</tool>