Normalization tests - sub WF

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Options

Plot a subset of samples separately?

Whether there should be created a series of plots separately for a subset of samples. Experimental design and subset lists need to be provided.

Select samples to be processed

Select names of the samples which should be normalized in the following steps. By default, all samples are selected

Normalization approaches to test

select the normalization approaches to test on the data specified below; you can set the list of methods independently next to the Data to be tested below

Graphs for all samples

Select which graphs do you want to create

Graphs for a sample subset

Select which graphs do you want to create for the given subset(s)

Experimental design

Provide an experimental design, e.g. for two samples consisting of 3 repetitions write "A, A, A, B, B, B"

Subsets

Enter subsets separated by comma, e. g. "A, B, C". If you want to plot two subset together enter their names separated by a plus sign. e. g. "A+B". Subset names need to correspond to "Experimental design".

Data to test: "prefix", "suffix", "name for graphs", "name for files", "norm. approaches (optional)"

comma separated list of values in quotation marks speficying one or more sets of data to test normalization method on; %%00010%%00010each line should describe one set of data; the information on one data should be provided in the following order:%%000101) common data prefix (e.g., "PG.Quantity+"), %%000102) common data suffix (e.g., "_log2"), %%000103) data name to be used in the figure subtitles next to the normalization method name (e.g., "PG.Quantity data"), %%000104) data name to be used in the filenames of exported figures next to the normalization method name (e.g., "diann-not-norm"). %%000105) list of comma separated normalization methods identifiers (integer specifying the norm. method as mentioned in the preceeding form field) to test on the given data concretely (e.g., "0,3"); the norm. methods checked above are used in case missing information here;%%00010%%00010the full data to test specification given the examples mentioned above would be (including the quotation marks): "PG.Quantity+", "_log2", "PG.Quantity data", "diann-not-norm", "0,3"

Prefix for figure file names

Enter a prefix (without a delimiter) which will be used at the beginning of figure file names. Default is blank for no prefix

Suffix for figure file names

Enter a suffix (without a delimiter) which will be used at the end of figure file names. Default is blank for no suffix.

Name of output folder

Enter the name of the folder in which output images will be stored

Name of output subfolder

Enter the name of the subfolder in which output images will be stored. This subfolder will be created inside the folder specified in the previous step. Leave empty, if you don't want to create any subfolder

Path to python3 executable

Absolute path to the python3 executable; do not change unless you want to use your own python environment outside the KNIME_docker_vnc container

Path to R executable

Absolute path to the R executable; do not change unless you want to use your own R environment outside the KNIME_docker_vnc container

Path to subworkflow

Enter path to subworkflow for actual normalization test execution relative to current workflow

Nodes

• String Input22 ×
• Component Input10 ×
• Component Output10 ×
• Single Selection9 ×
• Python Edit Variable8 ×
• String Configuration8 ×
• Integer Configuration5 ×
• Single Selection Configuration5 ×
• Boolean Configuration4 ×
• Boolean Input4 ×
• Multiple Selection Configuration4 ×
• Double Input3 ×
• Double Configuration2 ×
• Call Workflow Service1 ×
• Extract Context Properties1 ×
• Extract Table Dimension1 ×
• String to Path (Variable)1 ×
• Variable Expression1 ×

Extensions

• FeatureKNIME Base nodes
• FeatureKNIME Expressions
• FeatureKNIME Personal Productivity Tools
• FeatureKNIME Python 2 Integration (legacy)
• FeatureKNIME Quick Forms

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