With the Partek^® Flow^® Microarray Toolkit, you can import and analyze microarray data with the same ease as any sequencing analysis pipeline. This document covers the following parts: par

Supported

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Supported Platforms

Partek Flow supports popular gene expression microarray platforms including Affymetrix GeneChips (.CEL) and Illumina BeadChips (.idat). You can also import text output from Illumina Genome Studio in the form of tab-delimited text files with probe IDs and AVGSignal values. For the latter, each sample should correspond to one text file.

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The Convert to aligned reads task generates an Aligned reads data node. This then allows you to perform most tasks that can be performed on that data node type in Partek Flow. These include Quantify to transcriptome, Normalize counts and Differential gene expression (GSA) analysis. Please consult the documentation on a specific task for specific instructions on their use.

Additional Assistance

If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.

References

1. Affymetrix Whitepaper on Microarray normalization using Signal Space Transformation with probe Guanine Cytosine Count Correction. Accessed February 17, 2016
2. Irrizarry RA, Hobbs B, Collin F et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostat. 2003; 4:249-264.