Question: Cuffdiff significant genes
gravatar for Ali
4.1 years ago by
United States
Ali20 wrote:

I am new to RNA-seq analysis and wanted to know what is the best approach to filter out significant genes from the cuffdiff output. The issue I have is I don't have replicates so my understanding I can't use p-values, would it be enough to just rely on the log2 fold change? I appreciate your help.

rna-seq cuffdiff • 1.8k views
ADD COMMENTlink written 4.1 years ago by Ali20
gravatar for fubar
4.1 years ago by
fubar1.1k wrote:

Fold changes without replicates can support a descriptive analysis but inference using the conventional frequentist concept of statistical 'significance' is not possible without a reliable estimate of the variance for each individual transcript in each experimental group. This is true of any differential expression analysis method (eg see ), and has been widely discussed in more general forums - eg see and 

OTOH if you are a Bayesean, you could try although zero citations in 4+ years suggests that the author's prior beliefs have proven to be relatively uninformative....

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by fubar1.1k
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