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MACS2 result of FDR

Hello everyone As one of the output file of macs2 is in excel form which tells -log10(q-value) which is the FDR (False Discover Rate) I wan to ask whether the highest q-value is reliable or the lowest as every peak has its own -log10(q-value) In other words if -log10(q-value) is 10.08 of one peak is that mean that peak has high chance to be a false positive or its the other way around ?

Thanks in advance...

macs2 false discovery rate q-value chip-seq
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updated by GenoMax GenoMax • written by chaudharyc61 • chaudharyc61

Hi chaudharyc61, I have a question for you about that values,

how did you get that p-value?

My excel file does not have any columns for the p-value and the columns are this 

chr start   end length  abs_summit  pileup  #NOME?  fold_enrichment #NOME?  name

Thank you

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written by Morris_Chair Morris_Chair

While peak calling did you change the default p-value ?

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written by chaudharyc61 • chaudharyc61

1 answer

An FDR (or q-value) is an adjusted p-value, therefore the lowest q-value is the most significant. However, in this case you're not looking at q-values, but at -log10(q-value), in which case the highest number is more informative (because of that negative sign). For example, if q = 10^-10 that's a highly significant value, and -log10(10^-10) = 10, a high positive number.

The lowest q-value is most significant, and the highest -log10(q-value) is most significant.

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written by shawn.w.foley shawn.w.foley

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