[BioC] liandwong and mas5

[Laurent Gautier]

Hee Siew Wan wrote:
> Dear All,
>  
> I created a new cdf for the Dilution data:
> data(Dilution)
> i1 <- 13:16
> i2 <- 29:32
> i3 <- 45:48
> i4 <- 61:64
> i5 <- 77:80
> i6 <- 93:96
> m <- list(match = list(i1, i2, i3, i4, i5, i6))
> ids <- unique(hgu95av2probe$Probe.Set.Name[1:96])
> alt.cdf <- buildCdfEnv.matchprobes(m, ids, nrow.chip=640,
> ncol.chip=640, chiptype="HG-U95Av2", probes.pack="hgu95av2probe")
> new.dil <- Dilution[,1:2]
> validAffyBatch(new.dil, alt.cdf)
> new.dil.cdfenv <- alt.cdf at envir
> new.dil at cdfName <- "new.dil.cdfenv"
>  
> I encountered some problems when I tried to use the following expresso:
>  
> 
>>dil.lw <- liandwong(new.dil)
> 
> normalization: invariantset 
> PM/MM correction : subtractmm 
> expression values: liwong 
> normalizing...Error in smooth.spline(ref[i.set], data[i.set]) : 
>         need at least four unique `x' values
>  
> 
>>dil.mas <- mas5(new.dil)
> 
> background correction: mas 
> PM/MM correction : mas 
> expression values: mas 
> background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1)
>  
> What do those errors mean?

The errors are emitted by the functions doing the job behind the
wrappers... a call to 'traceback' call tell you more...

I would expect the pre-processing method you use to fail (or give
meaningless results) with such a small number of probes in use: you are
only handling 24 probes in your CDF !


> I'm using:
> R version 2.0.0
> affy version 1.5.8
> altcdfenvs version 1.1-9
> hgu95av2probe version 1.0
>  
> I'd appreciate any help. Thank you.
>  
> Regards
> SiewWan
> 
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