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@envir new.dil@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. Regards SiewWan

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@envir > new.dil@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

I've tried with larger probe pairs (207149 of ath1121501 array) but have the same problem. However, there are some probe sets with only 4 pairs. Could it be because of this small number of pairs per set? When I use traceback(); > traceback() 12: stop("need at least four unique `x' values") 11: smooth.spline(ref[i.set], data[i.set]) Does it mean that I need at least 4 intensity values? -----Original Message----- From: Laurent Gautier [mailto:lgautier@altern.org] Sent: Wed 17-Nov-04 10:38 PM To: Hee Siew Wan Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] liandwong and mas5 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@envir > new.dil@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >