Example Datasets (Optional)

Use one of the datasets and parameter settings below to understand how to run Cyber-T:

DNA Microarray Control + Experimental Data

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Quantitative Mass Spec Control + Experimental Data

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Complete P. falciparum Protein Microarray Data

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Low-replicate P. falciparum Protein Microarray Data

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Example RNA-Seq ENCODE Dataset

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Input File

File Format
File to upload

Note: Using the .

Reset

Fields delimited by
Delete rows with no label
Data row start
Number of label columns
Number of first condition columns
(e.g. number of control samples)
Number of second condition columns
(e.g. number of experimental samples)
Trouble uploading

Pre-Processing

Low Value Handling
Do nothing for low values
Set values less than to 0
Offset the values by the lowest value
Normalization
Normalization procedure

Bayesian Standard Deviation

Bayesian Analysis Parameters
Sliding window size
Bayesian confidence value
Blank or 0 gives non-Bayes regularized tests

Post-Processing

Posterior Probability of Differential Expression
Compute PPDE
Standard Multiple Hypothesis Testing Corrections
Compute multiple test corrections
Plotting Options
Plot with density estimate smoothing
Remove outliers before plotting

This analysis may take SEVERAL MINUTES to run, depending on the server speed, load, and number of data points analyzed.