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

[Warnes, Gregory R]

-----Original Message-----
From: Man, Michael 
Sent: Thursday, October 17, 2002 1:57 PM
To: Warnes, Gregory R
Subject: RE: [BioC] can't get summary.stat after "invariantset"
normalizat ion


It's version 1.0.  -m

-----Original Message-----
From: Warnes, Gregory R 
Sent: Thursday, October 17, 2002 1:16 PM
To: Man, Michael
Subject: RE: [BioC] can't get summary.stat after "invariantset"
normalizat ion


We will want to know which version of affy.  To find out do
'library(help=affy)'.  

-Greg

> -----Original Message-----
> From: Man, Michael 
> Sent: Thursday, October 17, 2002 12:45 PM
> To: 'Laurent Gautier'
> Cc: 'bioconductor@stat.math.ethz.ch'
> Subject: RE: [BioC] can't get summary.stat after "invariantset"
> normalizat ion
> 
> 
> 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
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> -- 
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 


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