[BioC] Channel splitting problem

[krasikov@science.uva.nl]

Hello,

I have a strange problem occured in spliting two-channel data into 
single channel set

The funny story is that the same code (adopted from limma user's guide)
works well for another set of microarrays.
All the differencies between two sets are first one is 8K Custom Agilent
and second one is 11K Custom Agilent. Both of them contains the same 
number of Probes (8091), but different number of Control spots.
As well probe annotation is slightly different. probeNames are the same 
and unique on both arrays, but corresponding geneNames are different. 
Most geneNames are missing in 8K microarray, whereas on 11K there are no 
missing values.
Maybe that is the reason for below described failure.
Has anybody any suggestions how to solve it?

# The Code:

 >targets <- readTargets(file=targetsFile, path=loadPath, sep="\t")
 >RG <- read.maimages(targets$fileName, path=loadPath, source="agilent", 
quote="")
# SpotTypes attachement:
 >spottypes <- readSpotTypes(file = "SpotTypeFile.txt", path = "qqq")
 >show(spottypes)
 >RG$genes$Status <- controlStatus(spottypes, RG)
# Removing Control spots:
 >isGene <- RG$genes$Status == "Gene"
 >RGc <- RG[isGene,]
# Normalization:
 >RGb <- backgroundCorrect(RGc,method="minimum")
 >MAlo <- normalizeWithinArrays(RGb, method="loess")
 >MAaq <- normalizeBetweenArrays(MAlo, method="Aquantile")
# Channel Spliting:
 >targets2 <- targetsA2C(targets)
 >u <- unique(targets2$Target)
 >f <- factor(targets2$Target, levels=u)
 >design <- model.matrix(~0+f)
 >colnames(design) <- u
 >corfit <- intraspotCorrelation(MAaq, design)

Here I'm getting long list of the same
"Warning message:
NaNs produced in: log(x)"

And then lmscfit doesn't work:
 >fit <- lmscFit(MAaq, design, correlation=corfit$consensus)
"Error in if (abs(correlation) >= 1) stop("correlation must be strictly 
between -1 and 1") :
         missing value where TRUE/FALSE needed"

Any suggestions?
Best wishes
Vladimir