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add additional reference to wiki article for MAD
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davidecarlson committed Oct 29, 2024
1 parent 3dd360f commit c231474
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2 changes: 1 addition & 1 deletion assets/differentialabundance_report.Rmd
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Expand Up @@ -726,7 +726,7 @@ iv_min_group_sizes <- unlist(lapply(informative_variables, function(x) min(table
if (any(iv_min_group_sizes > 2)){
cat("\n### Outlier detection {.tabset}\n")
cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below.\n")
cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below. For more on MAD, see [this wiki article](https://en.wikipedia.org/wiki/Median_absolute_deviation).\n")
}
foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -373,7 +373,7 @@
"exploratory_mad_threshold": {
"type": "integer",
"default": -5,
"help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. ",
"help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. For more on MAD, see https://en.wikipedia.org/wiki/Median_absolute_deviation.",
"description": "Threshold on MAD score for outlier identification",
"fa_icon": "fas fa-angry"
},
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