The tools listed below are all unsupported tools that have been developed internally at Thermo Fisher Scientific. They are not validated products and are provided as is and without warranty. Use of these tools is offered to those customers who understand and accept the associated terms and conditions and wish to take advantage of their potential to help manage and analyze GeneChip™ data. If any of these tools are to be used in a production environment it is the responsibility of the end-user to perform the required validation.

Analysis tools

Whenever possible, documentation is also provided to help provide guidance on use of the tools.

Affymetrix Power Tools contains a set of command-line tools for analyzing microarray data.

SNPolisher is an R package for post-process analyses of Axiom™ genotyping array results.SNPolisher generates cluster plots and density plots for each SNP to evaluate quality; generates region and plate plots for copy-number variation regions; reformats Axiom output for use with fitTetra; and reformats fitTetra output for classification and visualization in SNPolisher. The input files are the standard output files from Axiom arrays.

Both R and perl (64-bit) must be installed for SNPolisher to run. To install SNPolisher, download the zipped package file. This folder contains the SNPolisher R package file, the User's Guide, and the Quick Reference Card.  Unzip the folder, and then install the R package (SNPolisher_3.0.tar.gz). Follow the detailed instructions in the User Guide to install perl, R, and the SNPolisher package.

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