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indeed. i tried this today and the difference in FPKM values between the two normalizations was constant out to 4 decimal places.
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Oh I am very sorry! It is my problem: one set was processed slightly differently. :-(
Thanks, sdriscoll!
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sounds fishy. i wanna try this out and see what results i get. I'll report back unless of course someone comes in an explains it.
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cufflinks --compatible-hits-norm
Hi,
I am testing cufflinks with two different normalization methods: total-hits-norm and compatible-hits-norm. My understanding is that the only difference between these two methods is the FPKM denominator: one is the number of all hits, the other is the number of hits within the reference GTF. So the ratios of FPKM values calculated by two methods should be a single fixed number, which is the ratio of hits. But, the ratios I got is a distribution. Anybody have an idea of the exact meaning of compatible-hits-norm? Thanks!Tags: None
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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