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The most efficient way of importing array data would be to import them directly from your Partek Flow server. When you select this option, navigate to the folder containing your data files. Valid file types will be selectable for upload. Click on the files you would like to import into the project and select the Create sample button (Figure 1).

 

 

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Prefix Figure SubtitleText Importing microarray files into Partek Flow AnchorName Create Samples From Files

During the upload process, Partek Flow will determine the specific platform of your dataset. If they are commonly used chips, such as Affymetrix HTA arrays, the gene and transcript annotations associated with the platform will automatically be downloaded in the Library File Manager.

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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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Prefix Figure SubtitleText Converting Microarray intensity to Aligned reads AnchorName Microarray Data Node

Selecting an aligner will bring up the Microarray Conversion options page (Figure 4). Under the Select probe sequence file section, make sure that the correct Chip name is specified. For non-custom arrays, these should be set automatically to the platform detected upon importing the array.

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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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SubtitleText Advanced options for Microarray conversion AnchorName Advanced Options

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By default, this is set to take the mean of the intensities the probes and utilizes that to calculate the read count for the probe sequence. Clicking on the drop-down menu allows you to either turn off this feature (none) or use the median instead (Figure 6).

 

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SubtitleText Changing the way identical probes are consolidated AnchorName Image Options

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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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SubtitleText Changing the way identical probes are consolidated AnchorName Microarray Probes

This will display microarray probes aligned to the reference genome (Figure 9). By default, the probes are colored by their intensities with darker shades signifying higher probe intensities.

 

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SubtitleText Viewing probe intensities AnchorName Probe Intensities

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