Question: What Is Benjamini
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5.2 years ago by
mtyler.jason100
mtyler.jason100 wrote:

I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some potential pathways the genes belong to(KEGG pathways). However, I have a confusion what this column called benjamini is. What does it denote? Any suggestions?

gene-expression • 6.9k views
modified 5.2 years ago by Alex Reynolds23k • written 5.2 years ago by mtyler.jason100
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5.2 years ago by
Woa2.7k
United States
Woa2.7k wrote:

The column you're referring to contains 'corrected' p-value . The p-value is corrected for multiple hypothesis testing using the Benjamini-Hochberg method. There are other methods for such correction, the "Bonferroni-method" is one of them.

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Correct. Here's some useful background information. And here's a useful how-to which explains DAVID clearly, including the Benjamini column.

@Neilfws. Thanks for the information. However, I only know about t tests and pvalues. I don't have much knowledge about false discovery rate and all. The wiki article is a bit too technical for me. Can you guys give me something that can help me get better idea?

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imagine that an event has 10% of chance of occurring randomly, now if you were to repeat the experiment twice then it is obvious that the chance of observing the event has to be larger than 10%,

The easiest way to estimate it is to compute the chance of not seeing the event in both trials .9*.9 = 0.81 thus the chance of seeing at least one event is then 1-0.81 = 0.19 = 19%. So even though you started with 10% chance, the corrected probability of seeing the event is 19%