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Old 10-18-2010, 11:20 AM   #1
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Location: Washington DC

Join Date: May 2010
Posts: 7
Default Differential gene expression of gene clusters


I am analyzing RNA-Seq data. I have RPKM values for all the genes. The data set contains 7 samples. I am looking into genes associated with a specific pathway. This pathways has 6 gene clusters. I want to show that gene cluster 1 is expressed at higher level than the other clusters. How do I do that? The gene clusters have different number of genes. Is there any test that I can use? Packages like edgeR compare gene expression values for the same genes under different conditions. But I want to compare the expression of different genes. Can I somehow compare the different clusters to a housekeeping gene? Is there a statistical test that is used to do this?

Thank you.
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