Affymetrix Permutation-based Probe Level Estimation (APPLE).

Affymetrix Permutation-based Probe Level Estimation (APPLE).

• Goal:
  
  • Because of its cost, microarray experiments are frequently designed using a relatively small number of biological or technical replicates. This can result in low statistical power when the number of differentially expressed genes is inferred.
  • This worklfow investigates whether the statistical power of Affymetrix experiments can be increased, without the need to increase the number of hybridizations
• Input:

• Output:

Parameters to set GridMaAnova script: <o:p></o:p>

(1) data file url for maanova"data_file" input file example

(2) data file url for maanova "design_file" design file example

(3) A directory to save intermdiate results "temp_url"

(4) A log directory to save logs "log_url"

(5) A directory to save the permutations"perm_url"

(6) A directory to save the save output files "output_url"

Note: url stands for Uniform Resource Locator and thus have to follow the standard way of defining a url exp:
url for file locate on a gftp site: gsiftp://fs2.das3.science.uva.nl/home/adam/Apple
url for file locate on a http site: http://fs2.das3.science.uva.nl/home/adam/Apple

[More Details]

IMPORTANT: to RUN this workflow you need grid credentials which are acceptable by the Distibuted ASCI Supercomputer [DAS3]

• Contact the workflow author to get demo credentials
• to use this workflow for real input data, it is better to try to get approriate grid credentials
  • [How to get an account on DAS3]
  • [How to get credentials from the Dutch CA]