Mercurial > repos > ynewton > matrix_normalization
changeset 10:0c4dcd3980c1 draft default tip
Uploaded
| author | ynewton |
|---|---|
| date | Sat, 20 Oct 2012 02:28:54 -0400 |
| parents | 600872152be6 |
| children | |
| files | normalize.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/normalize.xml Sat Oct 20 02:28:37 2012 -0400 +++ b/normalize.xml Sat Oct 20 02:28:54 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="matrix_normalize" name="Matrix Normalize" version="1.0.0"> +<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": @@ -50,7 +50,7 @@ 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 +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> \ No newline at end of file