| Previous changeset 1:4973a2104cfd (2018-12-05) Next changeset 3:bdee2c2c484b (2019-03-08) |
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modified:
Intchecks/xml_intensity_check.xml |
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| diff -r 4973a2104cfd -r a7553caa2572 Intchecks/xml_intensity_check.xml --- a/Intchecks/xml_intensity_check.xml Wed Dec 05 10:27:45 2018 -0500 +++ b/Intchecks/xml_intensity_check.xml Mon Jan 14 08:17:26 2019 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="intens_check" name="Intensity Check" version="1.0.1"> - <description>Adding informations about intensities (mean fold change and missing values) in the Variable metadata</description> + <description>Adding information about intensities (mean fold change and missing values) in the variable metadata table</description> <requirements> <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> @@ -81,16 +81,15 @@ This tool performs two tests: a mean fold change calculation and the number of missing values. **Fold:** -The test calculates the mean fold change between two classes. It could be converted into a logarithm. -In the column name, the first class specified is the one used like numerator for the ratio. +The test calculates the mean fold change between two classes. It could be converted into logarithm. **Missing values:** -This tool calculates the number and the proportion of missing values in data matrix considering the class. +This tool calculates the number and the proportion of missing values in the data matrix considering the class. Missing values in numerical columns of data must be coded NA. **Two types of tests:** - | - Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class. - | - **Each class**: if the column class contains at least three classes and you want to test each of them. Otherwise, you have two classes and you want to choose the one used like numerator or denominator for the mean fold change. + | - Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class versus all the remaining samples without class distinction. + | - **Each class**: if the class columns contains at least three classes and you want to test each of them. Can also be used with only two classes, but you will not choose which class to put as numerator/denominator. ----------- Input files @@ -111,7 +110,7 @@ ---------- **Class column** - | Select the class column in Sample metadata. + | Select the class column in sample metadata table. **Type of test** | Two options: @@ -132,10 +131,11 @@ ------------ **Variable metadata file** - | Contains the previous columns in variable metadata and the new ones with fold tests, number and proportion of missing values. + | Contains the previous columns in variable metadata file and the new ones with fold tests, number and proportion of missing values. + | In the column names for fold, the first class specified is the one used like numerator for the ratio. **Graphs file** - | Contains barplots with the proportion of NA considering classes and boxplots with the fold values + | Contains barplots with the proportion of NA considering classes and boxplots with the fold values. </help> |