[BioC] liandwong and mas5

Hee Siew Wan g0203658 at nus.edu.sg
Tue Nov 16 09:50:23 CET 2004

Dear All,
I created a new cdf for the Dilution data:
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?
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.

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