[BioC] can't get summary.stat after "invariantset" normalizat ion

[Man, Michael]

R1.6 and Affy on IBM Thinkpad T22 . -m

-----Original Message-----
From: Laurent Gautier [mailto:laurent@cbs.dtu.dk]
Sent: Thursday, October 17, 2002 12:27 PM
To: Man, Michael
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: Re: [BioC] can't get summary.stat after "invariantset"
normalization



On Thu, Oct 17, 2002 at 11:24:24AM -0400, Man, Michael wrote:
> Any idea?  BTW, it works fine when I used unnormalized data.  -michael


Several even... which version of R and of the package are you using ?


L.


> 
> ###############################
> > tmp <- normalize.Plob.invariantset(latin)  # use the first CHIP as
> reference
> > latin.LiWong <- express(tmp, normalize=F, bg=subtractmm,
> summary.stat=li.wong)
> Background correcting
> Preparing Data
> Computing expression. This may take a while.
> Error in while (change > delta & iter < maxit) { : 
>         missing value where logical needed
> In addition: Warning message: 
> No convergence in inner loop after 50 in outerler tieration 4 
>  in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile,  
> 
> 
> > latin.LiWong <- express(tmp, normalize=F, summary.stat=li.wong)
> Background correcting
> Error in density(x, kernel = "epanechnikov", n = n.pts) : 
>         x contains missing values
> 
> 
> > latin.avdf <- express(tmp,normalize=F,bg=subtractmm,summary.stat=avdiff)
> Background correcting
> Preparing Data
> Computing expression. This may take a while.
> Error in var(x, na.rm = na.rm) : missing observations in cov/cor
> 
> 
> > latin.avdf <- express(tmp,normalize=F,bg=subtractmm,
> +                       summary.stat=function(x) apply(x,2,mean,trim=.2))
> Background correcting
> Preparing Data
> Computing expression. This may take a while.
> Error in psort(x, partial) : index 13 outside bounds
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