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Clicking 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.

Selecting Both the GCCN sequence correction transform checkbox normalizes and Scale intensity transforms were developed by Affymetrix [1]. GCCN scales the intensities with respect to the difference in probe affinity associated with Guanine and Cytosine (GC) contentv [1].The content. On the other hand, the Scale intensity transform was developed by Affymetrix to improve inter-platform comparisons between microarray and RNA-seq data. Specifically, the algorithm stretches the intensity distribution to a common range with a power law mapping that decompresses fold change ratios [1] . This ultimately simplifies fold change comparisons between different technologies. 

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 arrays are 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.

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