Theoretical question about the estimation of expression level (FPKM) in cufflinks-cuffcompare. In the tmap files produced by the Cufflinks suite of programs a confidence interval (actually, a probability interval?) is given. I've assumed that this is the confidence interval for the estimation of the FPKM. The cufflinks webpage give a reference to a paper by H. Jiang and W.H. Wong where the analytical steps towards determining an expression level are discussed (I might have to read this paper a couple of times more..).
I've been pondering about the best way to use the uncertainty in the expression levels when determining differential expression. This together with biological replicates should show the "real" variation of expression levels better than only using the point estimates from each sample (when using few biological replicates as most of us seem to be doing). Or are these confidence intervals only an indication of how uncertain the expression level is - not something that can be interpreted as an indication of the variation in expression levels?
Has anybody else had any success in using the confidence intervals?
Sorry for a confused thread, any suggestions would be highly appreciated!
Thanks,
Boel
I've been pondering about the best way to use the uncertainty in the expression levels when determining differential expression. This together with biological replicates should show the "real" variation of expression levels better than only using the point estimates from each sample (when using few biological replicates as most of us seem to be doing). Or are these confidence intervals only an indication of how uncertain the expression level is - not something that can be interpreted as an indication of the variation in expression levels?
Has anybody else had any success in using the confidence intervals?
Sorry for a confused thread, any suggestions would be highly appreciated!
Thanks,
Boel
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