[BioC] warnings from li wong summary method in expresso

[James W. MacDonald]

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 at 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.