Statistics and fold change equations in the Working Illustration

Background

In Cytobank, the Working Illustration is used to dynamically create figures to explore data. Besides a visual output to a figure, there is a statistical output that corresponds to the data being visualized. The statistics for an illustration appear below the plots in the Table of Statistics, and mimic the structure of the illustration itself.

The statistical output of the illustration can be customized in various ways. Click to jump to the section.

  1. The statistic (e.g. median, mean, percentile)
  2. The equation (e.g. raw or comparison between two samples)
  3. The comparison control (e.g. baseline for comparison equations)

 

Anatomy

(click to expand - Working Illustration statistics controls and example output)

 
Statistics available
  • Medians
  • Means
  • Standard Deviations
  • Variances
  • Minimums
  • Maximums
  • Event Counts
  • Percent in Gate
  • Coefficient of Variation
  • Channel Ranges
  • Geometric Means
  • Percentile
  • Percentile Distance (5 to 95)
  • Pearson R (X vs Y)

 

Equations to compare statistical data points

1. Raw (no comparison between data points)

For each statistic you will see the raw, untransformed data values, without any comparison to other data points. Currently there is not an option to display transformed raw statistical values. Notes on a workaround to this are at the following link in the article on heatmaps.

Value = x

2. Log10 Ratio

Each data point in the table of statistics reports the log10 ratio of itself compared to its control.

Value = log10(x/control)

or written differently...

Value = log10(x) - log10(control)

3. Fold

Each data point in the table of statistics reports the raw fold ratio of itself compared to its control. Data values are not transformed for the calculation.

Value = x / control

4. Log2 Ratio

Each data point in the table of statistics reports the log2 ratio of itself compared to its control.

Value = log2(x / control)

or written differently...

Value = log2(x) - log2(control)

5. Arcsinh Ratio

Each data point in the table of statistics reports the arcsinh ratio of itself compared to its control.

Value = arcsinh( (x - control) / scale_argument)

or written differently...

Value = arcinsh(x / scale_argument) - arcsinh(control / scale_argument)

The scale argument is taken according to the scale settings in the experiment. Even if the channel is not scaled by the arcsinh equation, the arcsinh ratio will still use arcsinh and the scale argument that is present in the scale editor at the time of the calculation.

6. Transformed Ratio

Each data point in the table of statistics reports the transformed ratio of itself compared to its control. The transformed ratio uses the scale settings of the channel being calculated.

Value = log10 ratio, arcsinh ratio, or fold, depending on scale settings. See sections above for an explanation of each equation.

7. Difference

Each data point in the table of statistics reports the raw difference of itself and its control.

Value = x - control

 

Comparison control

When a statistic and equation are chosen, a control needs to be elected as well. Click the toggle to highlight the controls to aid in interpretation (see image above). There are multiple options for control:

  • First Row
  • Column's Minimum
  • Column's Maximum
  • First Column
  • Row's Minimum
  • Row's Maximum
  • Table's First Cell
  • Table's Minimum
  • Table's Maximum

 



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