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Tools for differential expression are available on Gene/Transcript counts and on Normalized counts data nodes, under the RNA-Seq analysis section of the toolbox. The possibilities are as follows:

• Differential gene expression (GSA)
• Differential gene expression (ANOVA)
• Transcript expression analysis (Cuffdiff) – this option is only available on cufflinks quantification data node

The three options will be discussed below.

Differential Gene Expression (GSA)

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The table can be downloaded as text file when clicking the Download button on the lower-right corner of the table.

Additional Assistance

If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.
support@partek.com

References

[1] Benjamini, Y., Hochberg, Y. (1995). Controlling the false discovery rate: a practical
and powerful approach to multiple testing, JRSS, B, 57, 289-300.
[2] Storey JD. (2003) The positive false discovery rate: A Bayesian interpretation and
the q-value. Annals of Statistics, 31: 2013-2035.
[3] Auer, 2011, A two-stage Poisson model for testing RNA-Seq
[4] Burnham, Anderson, 2010, Model selection and multimodel inference
[5] Law C, Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology, 2014 15:R29.
[6] http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cuffdiff-output-files
[7] Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biology, 2010