[BioC] invarianset problem

Laurent Gautier laurent@cbs.dtu.dk
Tue, 14 Jan 2003 08:18:26 +0100


bug in expresso. Try the patch sent earlier on this mailing list
, the released version should be fixed soon.

https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-January/000672.html

Hopin' it helps,


L.



On Mon, Jan 13, 2003 at 03:34:27PM -0500, Tibor van Rooij wrote:
> When testing the invarianset method on the example as mentioned in the manual:
> 
> eset <- expresso(affybatch.example, normalize.method="invariantset",bg.correct=FALSE,pmcorrect.method="pmonly",summary.method="liwong")
> 
> I get the following error:
> 
> ......Error in quantile.default(sigma.theta, normal.array.quantile) : 
>         Missing values and NaN's not allowed if `na.rm' is FALSE
> In addition: Warning messages: 
> 1: No convergence achieved, too many outliers in: fit.li.wong(probes, ...) 
> 2: No convergence achieved, too many outliers in: fit.li.wong(probes, ...) 
> 3: No convergence achieved, too many outliers in: fit.li.wong(probes, ...) 
> 4: No convergence achieved, too many outliers in: fit.li.wong(probes, ...) 
> 5: No convergence achieved in outlier loop
>  in: fit.li.wong(probes, ...) 
> Error in name.levels(cdf) : Object "cdf" not found
> 
> Tibor
> _____________________________________
> Tibor van Rooij 
> Bioinformatician 
> McGill & Genome Quebec Innovation Centre
> McGill University Campus
> Tel:  (514) 398-2497
> 
> 
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Laurent Gautier			CBS, Building 208, DTU
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