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Old 09-29-2011, 07:42 AM   #1
brachysclereid
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Location: California

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Default Cufflinks, Cuffdiff, without replicates

Hi,

Can anyone help to understand how cufflinks/cuffdiff functions in the absence of replicates in layman's terms? I have read the website a few times and I'm afraid that I am missing something. How is the variance estimated in the absence of replicates for a given gene?

I am trying to figure out the mathematics of why you need a higher log fold change for a gene with low expression to get a significant p-value, whereas for a highly expressed gene a trivial change in fold change results in a significant p-value. It makes a lot of sense intuitively, but I am trying to understand this so that I can actually explain it.

Any help would be appreciated!
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Old 10-16-2012, 02:43 AM   #2
IBseq
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hi did you find any answer?

thanks,ib
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