Why mafdr works only for one threshold?
7 visualizzazioni (ultimi 30 giorni)
Mostra commenti meno recenti
hi! i have an array of p-values and i put him in mafdr() and it works fine. when i try to threshold this array of p-values and put the new array(array with values less than a threshold) in mafdr i get this error
??? Error using ==> mtimes Inner matrix dimensions must agree.
Error in ==> mafdr>storeyFDR at 239 fdr = pi0 * v./r;
Error in ==> mafdr at 190 [fdr, q, pi0_all, pi0, cs, rs] = storeyFDR(p, lambda, bootflag);
the only threshold that works for me is 0.05!!! i use matlab 2010a...whats wrong...?
0 Commenti
Risposte (2)
Enrico Glerean
il 13 Gen 2016
The error means that it fails to estimate the a-priori probability with the default value of Lambda [0.01:0.01:0.95].
You should specify a wider range of Lambda to run the command successfully. For example:
mafdr(p,'LAMBDA',[0.0001:0.01:0.95])
Please also note that you should not use fdr on thresholded p-values. By considering only the p values under 0.05 you are not controlling for multiple comparisons anymore and you are biasing your results (in neuroscience they often call this "double-dipping").
0 Commenti
Sean de Wolski
il 9 Set 2014
My guess is you've accidentally shadowed one of the earlier functions used by mafdr's storeyFDR so that it's calling your function instead of MATLAB's. This is a very common thing and is usually the cause of this type of error. Here are a few candidates, you can run which -all to tell you which one is being called and where the offending file is:
which -all sort
which -all min
which -all size
6 Commenti
Vedere anche
Categorie
Scopri di più su Bioinformatics Toolbox in Help Center e File Exchange
Prodotti
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!