WebSTAT - Free Web Statistics Partek Tutorial and Data Repository
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Partek Tutorial and Data Repository

The Partek Tutorial and Data Repository provides tutorials and data sets for analysis in Partek. Partek tutorials use specific data sets to show how to do data analysis and visualization. For the greatest learning benefit, they are designed to be used with their corresponding, provided data set. User Guides do not have a specific data set associated with them and are useful for learning general information. Note: The tutorials, user guides, and data sets in this section require Partek® Genomics SuiteTM. If you have any questions contact Partek support.

Gene Expression Next-Gen Sequencing
Exon

microRNA
Copy Number Integrated Genomics
Regulation
Partek Express User Guides White Papers Forum Series
FAQ
Baseline Files

Gene Expression


Affymetrix


Agilent


Illumina


NimbleGen


Affymetrix
  • Down Syndrome Study
    • Tutorial: Learn how to analyze a disease vs. normal study across multiple tissues with a focus on ANOVA contrasts and interactions (January 2009)
    • Data [56M]
    • CHP Files [3.3M]

  • Breast Cancer Study
    • Tutorial: Learn how to analyze a time/dose experimental design with a batch effect (August 2009)
    • Data [6M]





Agilent
  • Importing Data from Agilent's Feature Extraction Software
    • User Guide: Learn how to import Agilent gene expression and copy number data into Partek (December 2008)





Illumina
  • Gene Expression Analysis of an Age Study Using Illumina Microarray Technology
    • Tutorial: Learn how about comparing the performance of different ANOVA analysis and the impact on both genes and biological intepretation using Illumina microarray technology (June 2009)
    • Data [6.2MB]

GenomeStudio
  • Importing Gene Expression Data from GenomeStudio
    • User Guide: Learn how to export gene expression data from GenomeStudio into Partek GS by using the Partek Gene Expression Plug-in (April 2009)
    • The Partek Gene Expression Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Final Report Text File
  • Importing the Final Report from GenomeStudio for Gene Expression Data
    • User Guide: Learn how to import the Final Report from GenomeStudio into Partek GS (April 2008)





NimbleGen
  • Importing NimbleGen Data
    • User Guide: Learn how to import NimbleGen gene expression data into Partek (December 2008)





Survival Analysis

Next-Gen Sequencing


Illumina
ChIP-seq
  • Find IP Regions and Motifs Using ChIP-seq
    • Tutorial: Learn how to find IP regions and motifs within a ChIP-seq data set (June 2010)
    • Data [70MB]

RNA-seq
  • Analysis of RNA-Seq data within Partek GS using the RNA-Seq Workflow (June 2010)
    • Tutorial: Learn how to use the RNA-seq workflow within Partek GS to import, analyze, and visualize RNA-Seq data
    • Data [2.3GB]

SNP
  • Analysis of Nucleotide Variations within Partek GS (March 2010)
    • Tutorial: Learn how to detect nucleotide differences and annotate SNP calls with overlapping genes
    • Data

FAQ
  • Frequently Asked Questions for Next Generation Sequencing in Partek GS (March 2010)
    • FAQ: Find answers to some of the common next generation sequencing questions regarding Partek GS



Web Talks:

Exon




Web Talks:

Partek Video Information Series:
  • Differential Gene Expression and Alternative Splice Analysis of Affymetrix Exon GeneChips using Partek Genomics Suite (February 2008) [6 minutes]

microRNA


  • Analyzing microRNA Data & Integrating microRNA with Gene Expression Data in Partek
    • Tutorial: Learn how to analyze microRNA data within Partek, as well as how to integrate microRNA data with gene expression data in Partek (April 2009)
    • Data [370K]

Copy Number


General


Affymetrix


Agilent


CNAG


dChip


Illumina


Nimblegen



General Copy Number Topics
  • Optimizing Copy Number Segmentation in Partek
    • Tutorial: Learn how to find regions of copy number variation using Genomic Segmentation (April 2009)
    • Data [168M] (paired tumor/normal samples)





Affymetrix
SNP 6
  • Overlapping Copy Number with LOH
  • Copy Number Analysis in Partek GS v6.4 with FFPE Samples
    • User Guide: Learn the latest Copy Number workflows in Partek GS v6.4. Optional restriction fragment-length filters are shown to enhance performance on FFPE samples on SNP6 arrays (July 2008)

  • HapMap Sample: Learn how to do copy number analysis within a normal population
  • Allele Specific Copy Number Analysis with Cancer Sample
    • Tutorial: Learn how to analyze Allele Specific copy number (best used for primary tumor heterogeneous samples with possible normal contamination) (December 2007)
    • Data [168M] (paired tumor/normal samples)


Mapping 500K


Mapping 100K





Agilent
  • Importing Data from Agilent's Feature Extraction Software
    • User Guide: Learn how to import Agilent gene expression and copy number data into Partek (December 2008)





CNAG
  • Importing from CNAG
    • User Guide: Learn steps for importing data from CNAG into Partek (December 2007)





dChip
  • Importing from dChip
    • User Guide: Learn steps for importing data from dChip into Partek (December 2007)





Illumina
GenomeStudio
  • Importing Genotyping Data from GenomeStudio
    • User Guide: Learn how to export genotyping data from GenomeStudio into Partek GS by using the Partek Genotype Plug-in (April 2009)
    • The Partek Genotype Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Final Report Text File
  • Analyzing Illumina Copy Number Data in Partek
    • Tutorial: Learn how to import GenomeStudio data into Partek, generate paired copy number, identify regions of copy number, and generate a list of genes in a region (November 2008)





NimbleGen
  • Importing NimbleGen Data
    • User Guide: Learn how to import NimbleGen copy number data into Partek (December 2008)



Web Talks:
  • Copy Number & LOH of Cancer Samples on the Human SNP Array 6.0 Using Partek GS (October 2007)
  • Identifying Copy Number Variation using the Affymetrix SNP Array 6.0 and Partek (June 2007)


Partek Video Information Series:

Integrated Genomics


  • Colon Cancer Study: Exon
    • Gene-Level Analysis: Learn how to integrate exon data with Gene Expression Data (September 2007)

  • NCI60 Cell Line Study: Copy Number
  • Integrating and Correlating Gene Expression and Copy Number
  • Overlapping Copy Number with LOH



Partek Video Information Series:
  • Extending & Enhancing Expression Analysis through Integration with Genome-wide Assays (December 2008) [5 minutes]

Regulation Using Tiling Microarrays or Next-Gen Sequencing


Affymetrix
ChIP-chip
  • Finding IP Regions Using ChIP-chip and Integrating Regulation and Gene Expression Data
    • Tutorial: Learn how to analyze and integrate regulation and gene expression data within the same study (February 2009)
    • Data [84M]





Illumina
ChIP-seq
  • Finding IP Regions and Motifs Using ChIP-seq
    • Tutorial: Learn how to find IP regions and motifs within a ChIP-seq data set (April 2009)
    • Data [70MB]

GenomeStudio
  • Importing Methylation Data from GenomeStudio
    • User Guide: Learn how to export methylation data from GenomeStudio into Partek GS by using the Partek Methylation Plug-in (March 2010)
    • The Partek Methylation Plug-in for GenomeStudio can be found on the illumina•Connect download page.

Partek Express


Affymetrix


Agilent


Illumina


NimbleGen


Frequently Asked Questions


Affymetrix
  • Analyzing Affymetrix Data in Partek Express
    • Tutorial: Learn how to analyze a disease vs. normal study in Partek Express (May 2010)
    • Data





Agilent
  • Analyzing Agilent Data in Partek Express
    • Tutorial: Learn how to import Agilent gene expression and copy number data into Partek (May 2010)
    • Data





Illumina
  • Analyzing Illumina Data in Partek Express
    • Tutorial: Learn about gene expression analysis of an age study Using Illumina Microarray Technology (May 2010)
    • Data





NimbleGen
  • Analyzing NimbleGen Data in Partek Express
    • Tutorial: Learn how to import NimbleGen gene expression data into Partek Express (May 2010)
    • Data





Frequently Asked Questions
  • Frequently Asked Questions
    • FAQ (May 2010)

User Guides


  • Model Selection
    • User Guide: Understanding the Model Selection tool in Partek GS (April 2010)

  • Chromosome Viewer
    • User Guide: Understanding the Chromosome Viewer in Partek GS (March 2010)

  • Hierarchical Clustering
    • User Guide: Hierarchical Clustering Analysis of Microarray Data (January 2009)

  • Adding Annotations
    • User Guide: Learn how to associate a spreadsheet with an annotation file. Note: adding annotations is required if importing genomic data as a text (.txt) file (November 2010)

  • Creating a Sample Information File
    • User Guide: Learn steps to create your own sample information file, useful when importing large data sets (June 2008)

  • Displaying Genes from UCSC Annotation Files
    • User Guide: Learn how to display genes using a UCSC gene annotation file (June 2008)

  • Using .bed Files in Partek to Output Data
    • User Guide: Learn how to prepare a .bed file in Partek GS to output for upload to genome browsers, such as the UCSC Genome Browser (June 2008)

  • GO ANOVA
    • User Guide: Learn about Partek's GO ANOVA (August 2009)

  • GO Enrichment
    • Tutorial: Learn how to perform GO Enrichment analysis in Partek GS (March 2009)
    • Data [16M]

  • Understanding the Affymetrix QC metrics options
    • User Guide: Understand the many results and options of the QC metrics feature for Partek Genomics Suite and Partek Express (November 2010)



High-Throughput Screening Examples for use with Partek Screening Solution
Note: This tutorial and data set require Partek® Screening SolutionTM.

Normalization and Hit-Selection of an HTS Campaign
  • 384-Well Plate
    • Tutorial: Learn how to analyze 384-well plate data (September 2007)
    • Data [876K]

White Papers



RNA-Seq
  • Detecting Single Nucleotide Variations in Sequencing Data using Partek GS
    • White Paper: Learn about the algorithm that Partek GS uses to detect SNP/SNV from next generation sequencing data (May 2010)

  • Understanding RNA-Seq Methods in Partek GS
    • White Paper: Learn how Partek GS estimates expression levels of transcripts and quantifies alternative splicing of a gene (June 2010)




Copy Number
  • New Copy Number Processes in Partek Genomics Suite v6.5
    • White Paper: Learn about new copy number features in Partek GS, version 6.5 (January 2010)

  • Understanding Allele Intensity Import
    • White Paper: Learn how Partek GS imports Allele Intensity for Copy Number (January 2009)

  • Understanding Allele Specific Copy Number
    • White Paper: Learn how Partek GS calculates Allele Specific Copy Number (September 2008)

  • Understanding Loss of Heterozygosity
    • White Paper: Learn how Partek GS calculates Loss of Heterozygosity (June 2008)

  • Understanding Genomic Segmentation
    • White Paper: Learn about the genomic segmentation algorithm in Partek GS (June 2008)




ChIP-Chip
  • Detecting Regions of Significance
    • White Paper: Learn how Partek GS finds regions of binding in ChIP-Chip studies (December 2008)




ChIP-Seq
  • Fragment Length Analysis
    • White Paper: Learn how Partek GS estimates average fragment length in ChIP-Seq data (December 2010)

  • Detecting ChIP-Seq Peaks
    • White Paper: Learn how Partek GS detects peaks in ChIP-Seq studies (June 2010)

  • Motif Discovery
    • White Paper: Learn about the methods Partek GS uses to search for motifs in a set of genomic regions (April 2010)

Forum Series

Submit forum questions to Partek Workshops.





Past Forums


Biological Interpretation


Copy Number


Exon


Gene Expression


Integrated Genomics


microRNA


Next-Gen Seq


Regulation


Statistics


Partek Express



Biological Interpretation
February 9, 2010
  • Partek Biological Intepretation Web Forum: Biological Interpretation in Partek Genomics Suite This will include the use and understanding of gene ontology enrichment and GO ANOVA tools in Partek.

June 18, 2009
  • Partek Biological Intepretation Web Forum: using Partek to analyze gene expression data for biologically relevant changes. This will include the use and understanding of gene ontology enrichment and GO ANOVA tools in Partek.





Copy Number
December 3, 2009

July 21, 2009
  • Introduction to LOH and Allele Specific Copy Number Web Forum: presents the use of Partek to analyze SNP array data for allele specific aberrations

July 14, 2009
  • Intro to Copy Number Web Forum: understand how to use Partek to analyze copy number and CGH data for copy number variants

May 14, 2009
  • Partek Segmentation Web Forum: the application and optimization of Partek's recommended segmentation algorithm for copy number and CGH analysis





Exon
June 11, 2009
  • Partek Exon Web Forum: using Partek to analyze exon and whole transcript arrays with a focus on finding genes undergoing potential alternate splicing and differential transcript expression





Gene Expression
March 4, 2010
  • Partek Gene Expression Web Forum: The Gene Expression Workflow in Partek GS

May 28, 2009
  • Partek Gene Expression Web Forum: using the Gene Expression Workflow within Partek





Integrated Genomics
November 19, 2009
  • Reap the Benefits of Publicly Available Data - Integrated Genomics at Your Fingertips

November 12, 2009
  • See the Larger Picture: Integrate Gene Expression and Copy Number, with a Workflow





microRNA
October 29, 2009





Next-Generation Sequencing
December 09, 2010
  • Statistical Tools for Next Generation Sequencing Data Analysis

October 07, 2010

May 11, 2010
  • Integration of Next Generation Data in Partek® Genomics Suite™

March 25, 2010

December 16, 2009

November 5, 2009

September 3, 2009
  • RNA-Seq: Next Generation RNA Analysis Web Forum: explores the use of Partek to analyze next generation RNA expression data

July 28, 2009
  • ChIP-Seq: Next Generation ChIP Analysis Web Forum: presents the use of Partek to analyze next generation chromatin immuno-precipitation data





Regulation
May 4, 2009
  • Partek ChIP-Chip Web Forum: the application of whole genome arrays for peak detection





Statistics
November 18, 2010
  • Partek Statistics Web Forum: Clinical Applications & Microarray Data Analysis

October 26, 2010

June 22, 2010
  • Partek Statistics Web Forum: Statistical Analysis for Microarray and Next-Generation Sequencing Studies

January 21, 2010
  • Partek Statistics Web Forum: Experimental Design & Statistical Analysis for Microarray and Next-Generation Sequencing Studies





Partek Express
June 02, 2010
  • Partek Express Web Forum: The Most User-Friendly Gene Expression Microarray Analysis Software


Frequently Asked Questions


  • FAQ: Find answers to some of the common questions regarding Partek GS (January 2011)

Partek Distributed Copy Number and Baseline Files


Affymetrix


Illumina


Affymetrix
Partek GS v6.5*

*Note: The baseline files generated and used in Partek 6.5 are not compatible with Partek 6.4 and earlier.

Genome Wide SNP 6
270 GenomeWide SNP 6.0 HapMap Samples

794 GenomeWide SNP 6.0 HapMap Samples

Genome Wide SNP 5

Mapping 500K
  • Copy Number Baseline: Partek generated baseline from the 270 Mapping 500K Nsp/Sty HapMap samples available from GEO [21M]

Mapping 100K



Partek GS v6.4
Genome Wide SNP 6
  • Library Files: Includes Chromosome Variation, Chip Sequence Summary, and Fragment Length Summary files [44M]
  • Copy Number Baseline: Partek generated baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [12M]
  • Allele Ratio Baseline: Partek generated allele ratio baseline from the 270 GenomeWide SNP 6.0 HapMap samples [18M]
  • LOH Baseline: Partek generated LOH baseline from the 270 GenomeWide SNP 6.0 HapMap samples available from Affymetrix [3.8M]

Genome Wide SNP 5
  • Library Files: Includes Chromosome Variation, Chip Sequence Summary, and Fragment Length Summary files [34M]
  • Copy Number Baseline: Partek generated baseline from the 44 GenomeWide SNP 5.0 HapMap samples available from Affymetrix [5M]
  • Allele Ratio Baseline: Partek generated allele ratio baseline from the 44 GenomeWide SNP 5.0 HapMap samples [4.9M]


Mapping 500K
  • Copy Number Baseline: Partek generated baseline from the 270 Mapping 500K Nsp/Sty HapMap samples available from GEO [3M]
  • Allele Ratio Baseline: Partek generated allele ratio baseline from the 270 Mapping 500K Nsp/Sty HapMap samples [9.3M]


Mapping 100K




Illumina
Partek GS v6.5*

*Note: The baseline files generated and used in Partek 6.5 are not compatible with Partek 6.4 and earlier.

Illumina Human 1M


Illumina Human Omni1-Quad


Partek GS v6.4
Illumina Human 1M


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