James,

 I am actually using 16 hgu133plus2 arrays, so I find it a little strange.

Is there any way to know which probes failed (and how many totally) ?

Does anybody know if dChip is still freely available? Seems like there is no
link anymore
on the home page... I would like to cross check if the warnings are coming
up there as well

Cherrs

Marco


On 1/25/07, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> Hi Marco,
>
> marco zucchelli wrote:
> > Hi,
> >
> >  I am using in R the dChip method to normalize and summarize my micro
> > arrays.
> > I tried several times and I always get warnings. What this does mean?
> Are
> > the expression levels
> > returned reliable anyway ?
>
> If you don't have enough samples, the LiWong method won't converge for
> some of your probesets. Lack of convergence is usually not a good thing.
> I think the recommendation for using LiWong is to have at least 10 or 15
> samples.
>
> You might consider using a different method to summarize your data.
>
> Best,
>
> Jim
>
>
> >
> > I use R2.4.1 on linux redhat
> >
> > Marco
> >
> >
> > eset <- expresso(hum.brain.embryo, bg.correct =
> > FALSE,normalize.method="invariantset",
> > pmcorrect.method = "pmonly",summary.method="liwong")
> > normalization: invariantset
> > PM/MM correction : pmonly
> > expression values: liwong
> > normalizing...done.
> > 54675 ids to be processed
> > |                    |
> > |####################|
> > There were 50 or more warnings (use warnings() to see the first 50)
> >
> > Warning messages:
> > 1: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 2: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 3: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> > 4: No convergence achieved in outlier loop
> >  in: fit.li.wong(probes, ...)
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues.
>

	[[alternative HTML version deleted]]

