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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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Figure 4:  

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Prefix Figure SubtitleText The Microarray Conversion options page AnchorName Probe Sequence File Selection
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If for some reason you wish to override that selection, then click the Change selection link and select the chip name in the drop-down menu or select New chip… if you would like to upload a different chip annotation (Figure 5). Image Removed
Figure 5:

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Prefix Figure SubtitleText Selecting a different probe sequence file AnchorName Selecting a different probe sequence file
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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.

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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.Figure 6:

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SubtitleText Advanced options for Microarray conversion AnchorName Advanced Options
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The Specify annotation sequence format drop-down menu allows you to specify the format of the probe sequences associated with your microarrays. Please consult with the manufacturer of your microarrays to determine the exact specification of their probe annotation files. The options available for sequence annotation include:

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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).Figure 6:

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SubtitleText Changing the way identical probes are consolidated AnchorName Image Options
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The Sequence correction transform checkbox corrects intensity values for sequence-specific effects. It is turned off by default and we only advise that you select this option if there are wide differences in the GC content of your probes.

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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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Figure 8: Displaying microarray probes in Chromosome viewer

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SubtitleText Changing the way identical probes are consolidated AnchorName Microarray Probes
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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. Image Removed
Figure 9:

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SubtitleText Viewing probe intensities AnchorName Probe Intensities
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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.

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