[BioC] Channel splitting problem
krasikov@science.uva.nl
krasikov at science.uva.nl
Wed Nov 30 11:51:35 CET 2005
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
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