Question: DAVID: p-value and Benjamini correction interpretation
0
gravatar for Mel
2.8 years ago by
Mel0
Mel0 wrote:

Hi everybody!

I submitted a list of gene to DAVID Functional annotation chart tool. I decided to used EASE (p-value) cutoff of 0,05 (from the DAVID publication on Nature Protocols in 2009) and selected Benjamini correction. Now I have problems with results interpretation. Is the Benjamini value the (i/m)Q value? So if it is bigger than my p-value, is my term significantly enriched? Or should I interpret the Benjamini value like a new p-value corrected already and is it significant if it is <0.05? (It looks strange for a multiple comparison tests).

Thank u

ADD COMMENTlink modified 2.8 years ago by arta590 • written 2.8 years ago by Mel0

Hi Mel,

I was wondering about your chosen cut-off. Why did you choose to change from the default EASE 1.0 to 0.05 instead? I am trying to understand how the cut-off works to apply to my data. There doesn't seem to be much information about the exploration of this so how did that threshold work out for your data?

ADD REPLYlink written 11 months ago by kehoe20
2
gravatar for arta
2.8 years ago by
arta590
Sweden
arta590 wrote:

Benjamini correction is your false discovery rate and it is your adjusted p-value. So you should forget about your p-value after correction. So your test is significant if your adjusted p-value is smaller than criteria (such as 0.05 or 0.01). If you want to more about multiple testing, you can check here

ADD COMMENTlink written 2.8 years ago by arta590
0
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

Corrected p-values should be interpreted exactly the same as regular p-values (they're just corrected for multiple testing). Whether an adjusted p-value < 0.05 is significant is up to you (as is the case for unadjusted p-values).

ADD COMMENTlink written 2.8 years ago by Devon Ryan97k
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