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Once the samples have been uploaded, the Data tab will list each sample along with the Platform associated with each sample. If Affymetrix .CEL files were uploaded, it will also include the date that the array was scanned (Figure 2). This information may be helpful in assessing possible batch effects.

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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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).

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.

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).

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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