PIIKA 2.0 Legacy Version

Click here for help regarding the files and parameters listed below.
The sample files mentioned below correspond to the sample data mentioned in the paper describing PIIKA 2.

PIIKA 2 is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. If you would like to use it for commercial purposes, please contact us.

Step #1: Input files

	(Required) Main input file Contains the intensity values for your arrays. Sample file
	(Optional) Treatment-control combinations Specifies the treatment-control combinations in your dataset. Sample file
	(Optional) Treatment-control combinations for P-value visualizations Specifies the treatment-control combinations for P-value visualization files. Sample file

Step #2: Required parameters

(Optional) If you are using a commercial off-the-shelf array, choose it here, and the number of technical replicates and the number of peptides will be automatically filled in. If you are using a custom array, ignore this option.

Number of technical replicates per unique peptide on the same array

Number of treatments

Number of unique peptides on the array

Number of inter-array replicates

Note: if you entered a value greater than 1 for this option, please use the button below to indicate whether the inter-array replicates represent biological replicates or technical replicates.

Step #3: Optional parameters

Omit background subtraction?

If you choose "yes", instead of subtracting the background measurements from the foreground measurements, only the foreground measurements will be used (although the background measurements must still be provided).

Normalization method

Distance metric for hierarchical clustering

Linkage method for hierarchical clustering

Perform chi-square test?

***Note that the default choice for this option is now "no".***

Perform F-test?

Applies only if your dataset contains 2 or more biological replicates.

Perform biological subtraction before performing F-test?

Applies only if you are performing an F test.

Perform random tree analysis? (REMINDER: If you select this option, you must name your samples as described in the input guide (e.g., A-1, A-2, B-1, B-2, etc.). Also, please expect to wait a few hours for your job to finish if you select this option).

Note that to perform the random tree analysis, the number of inter-array replicates must be 1 (and thus the number of treatments must be equal to the number of arrays).

If you selected Yes for this option, please enter the number of random trees to generate (default = 2000).

Perform peptide subset analysis? (REMINDER: If you select this option, you must name your samples as described in the input guide (e.g., A-1, A-2, B-1, B-2, etc.). Also, please expect to wait a few hours for your job to finish if you select this option).

Note that to perform the peptide subset analysis, the number of inter-array replicates must be 1 (and thus the number of treatments must be equal to the number of arrays).

If you selected Yes for this option, please enter the number of random trees to generate for the random tree tests (default = 1000).

If you selected Yes for this option, please enter the maximum number of peptides to incude in a peptide subset. The smaller the number, the faster your job will complete (default = 50).

Value of alpha (false positive rate) for statistical significance testing

Estimated background probability that a peptide will be differentially phosphorylated

Step #4: E-mail address

(Required) Please enter your e-mail address here. Once your job is finished running, you will receive an e-mail with a link where you can download the results. Please note that your e-mail address may be saved for the purposes of tracking usage and of informing you of updates and bug fixes to PIIKA 2.

Step #5: Submit!

Image credit: Flickr user wildxplorer.