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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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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.

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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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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).

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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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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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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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