The RNA-Seq Normalization transformation allows you to apply RPK, RPM or RPKM normalization to your RNA-Seq experiments.
To apply the RNA-Seq Normalization transformation to an existing ArrayStar project, open the Edit Data Transformations dialog by selecting Data > Edit Data Transformations from the main menu.
Note: You may also apply the RNA-Seq Normalization transformation in the Set Up Preprocessing step of the Project Setup Wizard.
After the dialog opens, click the Add button to populate the dialog. From the Type drop-down menu, select RNA-Seq Normalization.
From the Normalization method section, select from:
•RPK – Reads assigned per kilobase of target. See RPK for more information.
•RPM – Reads assigned per million mapped reads. This normalization is available for RNA-Seq, ChIP-Seq, and miRNA experiments. See RPM for more information.
•RPKM – Reads assigned per kilobase of target per million mapped reads. See RPKM for more information.
Note: RPM is the only normalization method available for ChIP-Seq and miRNA experiments.