Cyber-T: Statistical Analysis for Paired Data
Example Paired Data Set 1 / Example Paired Data Set 2 (ln-transformed)

Input File
File to upload ( Format expected )
Fields delimited by

Delete lines with NULL Labels

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Comments
Please enter any text that you would like to have as a header for the analysis output

Please check if you want the standard header from Cyber-T in your files

Data Input

 Note: Please note that for the following fields, column numbering starts at 0. Row numbering starts at 1.
Separate the numbers by spaces, not commas or tabs.

Row number where data starts (if second row is where data starts, type 2, since row numbering starts at 1 - if left blank, row 1 is where data starts)
Label columns (names of genes or other identifying labels, e.g. 0)
Ratio data replicate columns - those that contain ratio data or the difference between log transformed expression levels derived from co-applying cDNA labelled with Cy3 (the control) and cDNA labelled with Cy5 (the treatment, for example). This data is derived from a single array and so it is analyzed by a different function. (e.g. 2 1 3)

Minimum non-zero replicates required (e.g. 3). If left blank, the number of values of experimental/ratio data will be used. What does this mean ?

  Check this button to take the natural log (ln) of uploaded values. Cyber-T assumes a ln-transformed data set because of issues of normality with untransformed datasets and will return valid results only if the dataset is ln-transformed.

Parameters for the Bayesian Standard Deviation Estimation

What do these mean?

Choose a sliding window size for approximating the variance of your values. How many total samples around the point of interest will give you a satisfactory estimate of the local variance?
Enter a confidence value here that applies to the Baysian variance estimate that you set immediately above. A decent default would be '10' or about 3 times the number of replicates per treatment (if # replicates is small). If left blank, the whole Bayesian estimate analysis will be skipped.
Paired expression value column number (Column containing the average expression levels for the sequences - e.g. if its the sixth column, type 5, since numbering starts at 0) What does this mean?

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