Dear listmembers.

I am trying to read in data using the methods described in the oligo
vignette, and then trying to visualize them using either SNPchip or
VanillaICE.

I am having some difficulties putting the output from oligo into the format
required for VanillaICE. I am using Affy 250k Nsp and Sty chips.

doing:
library(oligo)
fullFileName<- c("/home/me/chipA_Nsp.CEL")
aboutSamples <- data.frame(gender=c("female","female","male"))
rownames(aboutSamples)<-basename(fullFileName)
aboutVars<-data.frame(labelDescription="male/female")
rownames(aboutVars)<- "gender"
pd<-new("AnnotatedDataFrame", data=aboutSamples, varMetadata=aboutVars)

crlmmOut <- justCRLMM (fullFileName, phenoData=pd, verbose=TRUE)

gets me the crlmm information.
then:

preProc <- justSNPRMA(fullFileNames) # gives the SnpQSet
cn <- calculateCopyNumber(preProc) # gives the copynumbers
calls <- calls(crlmmOut) # gives the calls
callsConfidence <- callsConfidence(crlmmOut) # gives confidences


How do I now make a HmmSnpSet that VanillaICE needs?

I've checked the Bioc Mailist:
http://article.gmane.org/gmane.science.biology.informatics.conductor/14810/match=hmmsnpset
but that still doesn't make it clear. I think I'm missing something here.
Would someone please care to explain (probably the obvious, sorry for that)?

Thanks in advance.
MHB

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