Why mafdr works only for one threshold?

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...?

Answer 1

[Enrico Glerean]

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").

Answer 2

[Sean de Wolski]

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

[hmmaros]

Thank you for your reply! Im a little bit novice with matlab. So you tell me i must check all the functions which mafdr call inside by running which -all?

[Sean de Wolski]

I would stop in debug mode and then look at the previous lines:

dbstop if error

This will stop at the offending line. Look at functions a few lines up and which -all them to see which one is being called. If it's not MATLAB's version of the function, that is probably what is throwing the error.

[hmmaros]

and how i will check if it is MATLAB's version of the function?

[Sean de Wolski]

which -all functionname

If the path starts with the output from

matlabroot

Then it's part of MATLAB, otherwise it's yours.

[hmmaros]

i cant find something abnormal... when i run fdr for many times,then randomly it works one time...im so confused!

[Sean de Wolski]

Contact tech support, they can walk you through it.