Download Guide, Axiom Genotyping Solution Analysis

Chapter 1 | Introduction to Axiom® Data Analysis
7
(SNPolisher_package.zip). The zipped folder contains the R package file (SNPolisher_XXXX.tar.gz,
where XXXX is the release number), the user guide, the quick reference card, the help manual, the
license, copyright, and readme files, a PDF with colors for use in R, and the example R code and two
folders with example data for running in R. Note that this zipped folder is not a package binary for
installing in R. Users must unzip the file to extract the SNPolisher folder, which contains the tar.gz
package file. For instructions on R basics, installation, and usage of the R functions, including additional
function not discussed in this document, see the SNPolisher User Guide.
Both APT and GTC software tools require the files (collectively referred to as “analysis library files”)
listed in Table 1.1 to appropriately process and interpret the data. For Axiom arrays developed through
the Axiom custom design program, analysis files are made available from a secure file exchange server
to the owner of the array. The analysis files for Axiom catalog and expert arrays are available from either
the array product page (www.affymetrix.com) or through direct download via GTC.
Table 1.1 lists the names of all analysis files used to process Axiom genotyping arrays in GTC or APT.
An annotation file is an additional file not required for genotyping and is not listed below, but used in
GTC to display SNP annotations in SNP results tables, the cluster graph visualizations, and for some
export functionality. Annotation files are available for download through GTC or on the array product
page or the Secure File Exchange in the same locations as the analysis library files.
Table 1.1 Files Used For Analysis of Axiom Genotyping Arrays. <axiom_array> will be replaced with the actual name of the
array. <R#> will be replaced with the version# of the analysis files. For example, when <axiom_array>= Axiom_BioBank1 and <R#>=
r2 then <axiom_array>_96orMore_Step2.r<#>.apt-probeset-genotype.AxiomGT1.xml= Axiom_BioBank1_96orMore_Step2.r2.aptprobeset-genotype.AxiomGT1.xml.
Analysis Library Files
GTC
APT
<axiom_array>.r<#>.ps2snp_map.ps
N/A
Required
<axiom_array>_96orMore_Step1.r<#>.aptprobeset-genotype.AxiomGT1.xml
N/A
Required
<axiom_array>_96orMore_Step2.r<#>.aptprobeset-genotype.AxiomGT1.xml
N/A
Required
<axiom_array>.r<#>.cdf
Required
Required
<axiom_array>.r<#>.qca
Required
Required
<axiom_array>.r<#>.qcc
Required
Required
<axiom_array>.r<#>.step1.ps
Required
Required
<axiom_array>.r<#>.genetic_prior.txt
Required
Required
<axiom_array>.r<#>.AxiomGT1.sketch


<axiom_array>.r<#>.chrXprobes


<axiom_array>.r<#>.chrYprobes


<axiom_array>.r<#>.specialSNPs


Required for human genomes
Optional for non-human genomes
Required for mammalian genomes
N/A for non-mammalian genomes
Required for mammalian genomes
N/A for non-mammalian genomes
Required for human genomes
Required for non-human genomes if
gender calling is executed








Required for human genomes
Optional for non-human genomes
Required for mammalian genomes
N/A for non-mammalian genomes
Required for mammalian genomes
N/A for non-mammalian genomes
Required for human genomes
Required for non-human genomes
if gender calling is executed
<axiom_array>_LessThan96_Step1.r<#>.aptprobeset-genotype.AxiomGT1.xml
N/A
Required for small sample size
<axiom_array>_LessThan96_Step2.r<#>.aptprobeset-genotype.AxiomGT1.xml
N/A
Required for small sample size
Required for small sample size
Required for small sample size
<axiom_array>.r<#>.AxiomGT1.MODELS