[BioC] logical subscript too long in normalizeRobustSpline

[paul.boutros at utoronto.ca]

For anybody who replicates this error: Gordon was right -- I had the array 
layout mis-set.  When using debug, I uncovered a webset on debugging 
suggestions for R that was pretty helpful:
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/

Paul

> -----Original Message-----
> From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
> Sent: Thursday, November 04, 2004 5:26 PM
> To: paul.boutros
> Cc: bioconductor at stat.math.ethz.ch
> Subject: [BioC] logical subscript too long in normalizeRobustSpline
>
> 
> I don't know what the problem is.  If I was debugging this with
> my data I would:
>
> 1. Identify which array in a multi-array experiment is causing
> the error (by subsetting the RG
> object given to normalizeWithinArrays())
>
> 2. Check that the data for the array is ok, e.g., using summary(RG$R) etc
>
> 3. Try debug(normalizeRobustSpline), then re-run the
> normalization and step through the execution
> normlizeRobustSpline() line by line (by typing ENTER) to see
> where the error occurs.
>
> Gordon
>
> > Tue Nov 2 23:14:50 CET 2004
> > Hi again,
> >
> > Getting this error using robustspline normalization in limma:
> > Error in normalizeRobustSpline(object$M[, j], object$A[, j],
> layout, df = df,  :
> >         (subscript) logical subscript too long
> >
> > I'm on:
> > Win2k SP2
> > R 2.0
> > limma 1.8.8
> >
> > This isn't a general problem with robustspline, as I seem to be
> able to get it
> > to work on other datasets.  Any suggestions on how to debug?
> >
> > Paul
>
>