I would like to know, how to calculate p-values from log2 (expression ratio) value of given set of genes in a replicated microarray experiment.
Here's the entrance to one rabbit hole, enjoy: http://www.bioconductor.org/packages/2.9/bioc/vignettes/limma/inst/doc/usersguide.pdf
Sheesh, don't bite the newbies. If you're new to a field, you don't know the right keywords to search for (and get decent results).
I'll treat this as a sort of FAQ question, let's see if it pays off:
p-values are the results of applying a statistical test. The essential requirement is that the experiment is replicated (at least 3 repeated measurements is mostly recommended).
For a basic overview: http://en.wikipedia.org/wiki/Gene_expression_profiling#Statistical_analysis
There are many software tools that can do these calculations (even Excel could do a simple t-test), but R and Bioconductor contain the largest collection of microarray test-tools:
multtest for dealing with the multiple testing problem
For differential expression analysis of RNA-sequencing, there are e.g.:
cuff-links/-diff (stand alone)
here's the complete list.
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