[BioC] Problem with limma backgroundCorrect function

Gordon K Smyth smyth at wehi.EDU.AU
Wed Dec 15 13:20:00 CET 2004

Yes, this is a bug.  The code was intended to be !is.finite(sigma) rather than
!is.infinite(sigma).  Thanks for finding this.  Will be fixed in limma version 1.8.14.

The bug affects only the starting values of fit.normexp(), not the final parameter values.  So
whenever the function converges, the bug will have had no final effect.  (I just tested the
function on a set of 34 arrays with and without the bug fix to confirm this.)

What the bug will have done is to increase the frequency of convergence failures.  Convergence
failures lead to arrays with almost everything set to NA, so are easily recognisable.  limma has
been trapping and reporting convergence failures in fit.normexp() since version 1.8.10.  Hopefully
they will now occur less often.


> Date: Wed, 15 Dec 2004 14:06:39 +1100
> From: michael_kirk at wmi.usyd.edu.au
> Subject: [BioC] Problem with limma backgroundCorrect function
> To: bioconductor at stat.math.ethz.ch
> I recently started to use the backgroundCorrect function in limma
> with the "normexp" method, as suggested in the user guide so as to
> avoid the problem of zero or negative intensities. When analyzing
> a set of about a dozen arrays, one of them ended up with NA M values
> for every gene after the call to backgroundCorrect.
> Looking at the code it transpires that backgroundCorrect calls
> fit.normexp (when method="normexp"), and the code for fit.normexp
> contains the following:
>     sigma <- sqrt(mean((f[f < mu] - mu)^2, na.rm = TRUE))
>     if (!is.infinite(sigma) || sigma < 1)
>         sigma <- 1
> I.e. sigma is set to 1 unless it is +Inf, which I suspect might
> not be what was intended.  Removing the ! from is.infinite as a
> test, and reanalysing the array which got set to all NAs, I do
> get reasonable looking numbers back (not all NAs).
> If this is a bug, I wonder what effect would it have had on other
> data - would all data analyzed with backgroundCorrect in this way
> be compromised?
> Michael

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