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How To Compute P-Values From Gene Expression Data?

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.

gene statistics p-value differential
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updated by Michael Dondrup Michael Dondrup • written by Sanchita Gupta • Sanchita Gupta

nice, many people would like to know this, they might normally tend to read books or articles or search the internet. have a nice day

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written by Michael Dondrup Michael Dondrup

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).

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written by Michael Kuhn Michael Kuhn

And then? do you want to write up a tutorial each time a newbie asks about what a p-value is? But you are right, the keywords are: statistical test, gene-expression, differential expression analysis, p-value. Still no need to re-open this.

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written by Michael Dondrup Michael Dondrup

1 answer

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.:

• 114 views • link
written by Michael Dondrup Michael Dondrup

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