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• Supported platforms
• Importing microarrays
• Converting microarray intensities to aligned reads
• Downstream tasks
• Viewing probes in the chromosome viewer

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.

Data Import

To import microarray files into a project, go to the Data tab of the project and select the Import Data button. If the data is not already in an existing Partek Flow project, select the Automatically create samples from files button. You will be presented with three different ways to upload your data files:

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You can now add additional sample attributes to your microarray project. For more information on how to set up your project, please refer to the documentation on Creating a project.

Custom annotations

Partek Flow also supports custom-made Affymetrix and Illumina arrays. Once the data files have been uploaded, you will also need to supply a custom annotation file which contains information on the probe sequences associated with the array. Please refer to the document on Importing Custom Microarrays for additional information on how to create and upload these annotations.

Conversion to Aligned Reads

Once the microarray data has been uploaded, the Microarray intensity data node will appear in the Analyses tab. To convert this data to aligned reads, select the Microarray intensity data node and select the aligner you would like to use for conversion (Figure 3).

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In the Select coverage depth section, you can set the nominal read coverage depth for your array. This is by default set at 20 million reads. However, you can adjust this number for better accuracy or if you are evaluating low-expressing genes. If you are comparing the microarray data with a corresponding NGS dataset, you can use this option to scale your data to a more comparable order of magnitude. Take note that setting this to a higher number will result in longer computation times overall.

Advanced options

Clicking the Configure link under the Advanced options section to view the advanced options that can be modified. These are generally transformations applied to microarray data (Figure 6). Note that both interrogating and control (if present) probes are used during fitting and adjustment.

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The RMA background transform check box applies robust multi-array average (RMA) normalization to your microarray samples [2]. This is a well-accepted method of background correction for microarray intensities.
The Quantile normalization check box performs quantile normalization on all microarray intensities. This is important in making sure that signals from any two arraysare comparable.
Any combination of these advanced options can be saved as its own option set. Once the option set has been created, it will be available in the Option set drop-down menu for use in future projects.
After you have finished configuring all microarray conversion options. Click the Next button to configure the parameters for the aligner you have chosen to use. Please refer to the documentation on Alignment for more information about configuring aligners.

Visualizing Microarray Probes

To visualize microarray probes in Partek Flow's Chromosome viewer, click the Select tracks button at the top left corner of the viewer. Select the Probe intensities check box to display microarray probes (Figure 8).

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Clicking a specific probe will display additional information about that probe including mapping position and sequence length. If the probe intensities are consolidated for specific categorical attributes, the average probe intensity is also displayed. For more details on how to use the Chromosome viewer, please consult its documentation.

Downstream Tasks

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.

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