[BioC] Warning message with dChip method

Tue Mar 16 20:44:14 MET 2004

from the li.wong help:

 Notice that this iterative algorithm will not always converge. If
     you run the algorithm on thousands of probes expect some
     non-convergence warnings. These are more likely when few arrays
     are used. We recommend using this method only if you have 10 or
     more arrays.

also notice you are not running dChip. also from the help file:

  This is Bioconductor's implementation of the Li and Wong
     algorithm. The Li and Wong PNAS 2001 paper was followed. However,
     you will not get the same results as you would get with dChip.
     dChip is not open source so it is not easy to reproduce.

On 
Tue, 
16 Mar 2004, Lizhe Xu wrote:

> I got the following message when runing dChip, should I ignore the warning message or ignore the method?
> 
> > dDataA<-expresso(DataA, bgcorrect.method="mas", normalize.method="invariantset", pmcorrect.method="pmonly", summary.method="liwong")
> background correction: mas 
> normalization: invariantset 
> PM/MM correction : pmonly 
> expression values: liwong 
> background correcting...done.
> normalizing...done.
> 22283 ids to be processed
> Warning message: 
> No convergence achieved in outlier loop
>  in: fit.li.wong(probes, ...) 
> Warning message: 
> No convergence achieved in outlier loop
>  in: fit.li.wong(probes, ...) 
> 
> Thanks.
> 
> Lizhe
> 
> -----Original Message-----
> From: bioconductor-request at stat.math.ethz.ch [mailto:bioconductor-request at stat.math.ethz.ch]
> Sent: Tuesday, March 16, 2004 11:29 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: Bioconductor Digest, Vol 13, Issue 36
> 
> 
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> 
> Today's Topics:
> 
>    1. RE: MOE430 A and B - bug? (Jose Duarte)
>    2. Re: Where are the new metadata packages (John Zhang)
>    3. canine annotation library package (LIANHE SHAO)
>    4. BioConductor: Affy Package (Julius Viloria)
>    5. Re: warning messages in gcrma (paolo.sirabella at uniroma1.it)
>    6. QualityWeights (using limma) (joycel_balaena.bio.vu.nl)
>    7. Re: Where are the new metadata packages (Jeff Gentry)
>    8. Canine annotation package (LIANHE SHAO)
>    9. RE: Quantile normalization vs. data distributions
>       (Arne.Muller at aventis.com)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: 16 Mar 2004 15:05:19 +0000
> From: Jose Duarte <jose.duarte at human-anatomy.oxford.ac.uk>
> Subject: RE: [BioC] MOE430 A and B - bug?
> To: Aedin <aedin.culhane at ucd.ie>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <1079449519.20677.30.camel at fgu013.anat.ox.ac.uk>
> Content-Type: text/plain
> 
> I am getting exactly the same error in aafGO:
> 
> > a<-aafGO(probeids,"moe430a")
> Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
> 
> This is when using version 1.5.0 of the moe430a metadata package. In a
> different machine with version 1.4.0 this works alright. annaffy version
> is 1.0.3 in both.
> 
> Thanks
> 
> Jose
> 
> 
> On Mon, 2004-03-15 at 17:04, Aedin wrote:
> > Hi
> > I am having problems using annaffy GO (aafGO) annotations on these chips? I
> > have updated my chip annotation files, and GO library, but still get
> > 
> > > a<-aafGO(rownames(chipA), "moe430a")
> > Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found
> > 
> > Thanks for your help,
> > Aedin
> > 
> > -----Original Message-----
> > From: bioconductor-bounces+aedin.culhane=ucd.ie at stat.math.ethz.ch
> > [mailto:bioconductor-bounces+aedin.culhane=ucd.ie at stat.math.ethz.ch]On
> > Behalf Of Ben Bolstad
> > Sent: 15 March 2004 14:17
> > To: peter robinson
> > Cc: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] MOE430 A and B
> > 
> > 
> > you need to read in the type A and type B files into separate affybatch
> > objects.
> > 
> > eg
> > 
> > my.Data.A <-
> > ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel"))
> > 
> > my.Data.B <-
> > ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel"))
> > 
> > Ben
> > 
> > 
> > 
> > 
> > 
> > 
> > On Mon, 2004-03-15 at 04:20, peter robinson wrote:
> > > Dear List members,
> > >
> > > I would like to use the affy package to analyze data from MOE430A and -B
> > > chips. I tried to read in data from both types of chips at once using
> > > data <- ReadAffy(widget=T)
> > > and then reading in 3 MOE430A and 3 MOE430B CEL files.
> > > I got the error message:
> > > "Cel file does not seem to beo of 430MOEA type" when the script tried to
> > input
> > > data from a 430MOEB Cel file. I had imported the CDF and annotation
> > packages
> > > for both types of chip.
> > > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
> > >
> > > Thanks for any advice/tips!
> > >
> > > Peter
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > --
> > Ben Bolstad <bolstad at stat.berkeley.edu>
> > http://www.stat.berkeley.edu/~bolstad
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> > _______________________________________________
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>