Question: How To Compute P-Values From Gene Expression Data?
2
gravatar for Sanchita
7.5 years ago by
Sanchita30
Sanchita30 wrote:

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.

ADD COMMENTlink modified 3.3 years ago by Michael Dondrup46k • written 7.5 years ago by Sanchita30
4

Here's the entrance to one rabbit hole, enjoy: http://www.bioconductor.org/packages/2.9/bioc/vignettes/limma/inst/doc/usersguide.pdf

ADD REPLYlink written 7.5 years ago by Steve Lianoglou5.0k
2

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).

ADD REPLYlink written 7.5 years ago by Michael Kuhn5.0k
17
gravatar for Michael Dondrup
7.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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: e.g.:

For differential expression analysis of RNA-sequencing, there are e.g.:

ADD COMMENTlink modified 3.3 years ago • written 7.5 years ago by Michael Dondrup46k
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