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Posts by ddjima2014
... I haven’t worked with hybrid genome before, I am trying to create a custom genome to align RNA-Seq that was generated from hybrid mouse. Would you please guide me how to create a custom genome for two hybrid mouse? The strains are C57BL and 6NJ. I have aligned to the mouse reference genome (C57BL) ...
... I have a signature genes similar to pam50 (breast cancer signature) from other tumor. How should I use "intrinsic.cluster" OR "intrinsic.cluster.predict()" function in genefu package to do nearest centroid classifier to assign the tumor subtype? I have a matrix like this that define the subtype: ...
Answer: A: RNAseq data and PAM50 method
... Can you guys help. I have a signature genes similar to pam50 from other tumor. How should I use "intrinsic.cluster" OR "intrinsic.cluster.predict()" function in genefu package to do nearest centroid classifier? I run intrinsic.cluster() with the 3 centroid with the signature genes, BUT I got c ...
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