RGG textfield has incorrect default value

I have the following R template:

<!--1. Global Metrics QC and Analysis -->           
<h3 text="$$$TEMPLATE_NAME$$$" aligment="center" span="full"/>           
<separator label="Description" span="full"/>           
<labelarea span="full">$$$TEMPLATE_NAME$$$</labelarea>           
<gaprow height="1"/>           
<!-- 2. Configuration-->           
<gaprow height="2"/>
<separator label="Slides" span="full" />
slides = c(<panellistbox label="Slides" items="$$$DOMAIN('slide_dir')$$$" visible-row-count="6" span="full"/>)
<separator label="File Parameters" span="full" />
<filechooser var="clinicalDataFilePath" label="Clinical Data File Path:" fileselection-mode="files-only" span="full" />
<filechooser var="gmNamesFilePath" label="GM Names File Path:" fileselection-mode="files-only" span="full" />
<separator label="Quality Control Parameters" span="full" />
<textfield var="epiNumThreshold" label="EPI Threshold:" data-type="number" default-value="50" size="5" />
<textfield var="pctNegThreshold" label="Negative Threshold (%):" data-type="number" default-value="95" size="5" />           
<textfield var="avgIntensityThreshold" label="Avg. Intensity Threshold:" data-type="number" default-value="10" size="5" />           
<separator label="SR1 Biomarker Selection Parameters" span="full" />
<textfield var="qvalue_feature_high_limit_sr1" label="QValue Feature High Limit:" data-type="number" default-value="0.1" size="5" />
<textfield var="slope_shrinkage_low_limit_sr1" label="Slope Shrinkage Low Limit:" data-type="number" default-value="0.8" size="5" />
<separator label="SR2 Biomarker Selection Parameters" span="full" />
<textfield var="sr2_qvalue_feature_high_limit" label="QValue Feature High Limit:" data-type="number" default-value="0.3" size="5" />
<textfield var="sr2_slope_shrinkage_low_limit" label="Slope Shrinkage Low Limit:" data-type="number" default-value="0.8" size="5" />
<separator label="Bootstrap Parameters" span="full" />
<textfield var="b" label="B:" data-type="number" default-value="10" size="5" />

When I first select the template the text field "qvalue_feature_high_limit_sr1" is displayed with the default value of 0.1, which is correct.  Now if I re-configure the node the same field is displayed with a value of 0.3 when 0.1 was previously selected.  Any ideas?



Hi Hathawa,

yes, I can reproduce this. The problem lies in RGG (I think!?): all labels have to be unique in a template. You have twice the labels "QValue Feature High Limit:" and "Slope Shrinkage Low Limit:" in your template. Somehow RGG doesnt treat the label just as a text to display, but rather as an variable for the GUI element. If you use a label more than once, then some things get mixed up. (dont ask me the details, I am not a programmer)


If you change the labels to "QValue Feature High Limit SR1:" and "QValue Feature High Limit SR2:" the the RGG will remember what was configured.