[BioC] expresso errors for MBEI

[Rafael A. Irizarry]

if someone else doesnt solve your problem:

immediately before the call to expresso that gives errors try

print(data)
class(data)
test1 <- normalize(data,method="invariantset")
test2 <- expresso(data,normalize.method="quantiles",bg.correct=FALSE,
       pmcorrect.method="pmonly",summary.method="liwong")

and tell us what you get back.


rafael
ps the non convergence warning is something you have to live with when 
using li and wongs method. sometimes their algorithm doesnt converge. its 
usually a very small percentage of the probesets though.

On Wed, 7 May 2003, Ann Hess wrote:

> I am trying to use the expresso command to get MBEI values.  I get the
> following errors.  Note that I was able to use expresso to get RMA and MAS
> values for the same data without any errors.  Any suggestions?
> 
> **I am using R version 1.6.2 and affy version 1.1.1.
> 
> > eset3<-expresso(data,normalize.method="invariantset",bg.correct=FALSE,
> 	pmcorrect.method="pmonly",summary.method="liwong")
> 
> normalization: invariantset
> PM/MM correction : pmonly
> expression values: liwong
> normalizing...done.
> 7129 ids to be processed
> .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 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, ...)
> 5: No convergence achieved in outlier loop
>  in: fit.li.wong(probes, ...)
> Error in name.levels(cdf) : Object "cdf" not found
> 
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