# [Eeglablist] FDR parameters

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Thu Jan 26 14:00:21 PST 2017

```Dear Nils,

I pasted the results from 'help fdr'. Apparently, it takes only two inputs,
p-values and alpha. So if you use any value other than p-values, that
should be alpha.

Makoto

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> help fdr
fdr() - compute false detection rate mask

Usage:
>> [p_fdr, p_masked] = fdr( pvals, alpha);

Inputs:
pvals   - vector or array of p-values
alpha   - threshold value (non-corrected). If no alpha is given
each p-value is used as its own alpha and fdr corrected
array is returned.
fdrtype - ['parametric'|'nonParametric'] fdr type. Default is
'parametric'.

Outputs:
p_fdr    - pvalue used for threshold (based on independence
or positive dependence of measurements)
p_masked - p-value thresholded. Same size as pvals.

Author: Arnaud Delorme, SCCN, 2008-
Based on a function by Tom Nichols

Reference: Bejamini & Yekutieli (2001) The Annals of Statistics
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

On Wed, Jan 25, 2017 at 12:55 AM, Nils Hachmeister <
nils.hachmeister at uni-bielefeld.de> wrote:

> Hi everyone,
>
> I'm using the study structure and aim to generate different plots
> including statistical testing (non-parametric) with multiple comparison
> correction, namely FDR. I used FDR before (in a context unrelated to
> eeglab) and it is my understanding that you pass a parameter alpha to it.
> FDR returns a (common) threshold for p-values which guarantees that the
> expected rate of type-I errors among all rejections of the 0-hypothesis is
> smaller or equal to alpha.
>
> Now, in the statistics menu in the eeglab gui and the documentation at
> https://sccn.ucsd.edu/wiki/Chapter_06:_Study_Statistics_and_
> Visualization_Options I cannot really find that notion. There is no
> mention of a parameter nor any constraints regarding the rate of type-I
> errors. However, I noticed that when passing a value to the edit-field
> labeled threshold the results change pretty much in a way consistent with
> that field being used as FDR-alpha. But from the documentation I cannot
> confirm this assumption. Can anybody here confirm this?
>
> Best
>
> Nils
>
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--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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