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Hello:
Could you please help me figure out how to get a certain quantitative metric from Cufflinks/Cuffdiff.
Suppose I want to stop at quantification without going for differential expression testing. Such situation can arise when I have only one sample for one condition and there is nothing to test it against. What I need is some measure of uncertainty for the FPKM values that I get after quantification. I attached an excerpt from an old version of Cufflinks manual where they seem to have such measure, denoted by Var[FPKM_t] on p 13.
Could you suggest how I could get Var[FPKM_t] (or a similar measure of uncertainty) explicitly from any version of Cufflinks/Cuffdiff.
Could you please help me figure out how to get a certain quantitative metric from Cufflinks/Cuffdiff.
Suppose I want to stop at quantification without going for differential expression testing. Such situation can arise when I have only one sample for one condition and there is nothing to test it against. What I need is some measure of uncertainty for the FPKM values that I get after quantification. I attached an excerpt from an old version of Cufflinks manual where they seem to have such measure, denoted by Var[FPKM_t] on p 13.
Could you suggest how I could get Var[FPKM_t] (or a similar measure of uncertainty) explicitly from any version of Cufflinks/Cuffdiff.