Good morning,

I apologize for troubling the list. I have researched this issue for a day,
and spent some time troubleshooting but am unable to locate the answer. I am
using R 2.7.2, Bioconductor 2.2 with oligo package version 1.4 and SNPchip
1.4. I am new to high throughput SNP analysis.

My goal is to perform copy number / LOH analysis on tumor tissue samples
processed with Affymetrix 100K SNP chips.

Question :
1. My understanding is that I need an oligoSNPset class object to work on in
SNPchip. How do I use oligo to generate an oligoSNPset class object?
(genotypes + copy number). In a related 2nd question, I need to merge the
oligoSNPset class objects from Xba and Hind CEL files for 100K Affymetrix
chips - I can only find online how to do that for SnpCallSetPLUS class
objects.

2. How may I merge the 2 separate SnpQset class objects from justSNPRMA
(Hind and Xba chips) from dual chip Affymetrix 100K SNP chips? How may I use
that object in SNPchip for copy number analysis, if possible?


DETAILS:

1. I have no problems with the vignette in SNPchip, and viewing the plot.

> library(SNPchip)
> data(sample.snpset)
> sample.snpset
> snpset <- sample.snpset[chromosome(sample.snpset) =="1",1]
> graph.par <- plotSnp(snpset[,1])
> graph.par$label.cytoband <- FALSE
> graph.par$use.chromosome.size <- TRUE
> graph.par

Now sample.snpset belongs to class oligoSnpSet.

I tried, but can only find out how to create objects of SnpCallSetPlus class
(genotype calls) from CEL files, using combine to merge Xba and Hind
results.

> library(oligo); library(hapmap100kxba); library(hapmap100khind)
...
> xba <- justCRLMM(fullFilenames, phenoData = pd,verbose = FALSE)
> hind <- justCRLMM(fullFilenames, phenoData = pd,verbose = FALSE)
...
> callset <- combine(xba,hind)
> str(callset)
Formal class 'SnpCallSetPlus' [package "oligoClasses"] with 6 slots

I have looked at the PDF file in oligoclasses showing that SnpCallSet
belongs to a different class (genotype calls) compared to oligoSnpSet
(genotype calls and copy number estimates), but I am still uncertain, I am
quite new to this sort of analysis. I have read a comment in the oligo
vignette
www.bioconductor.org/packages/2.4/bioc/vignettes/SNPchip/inst/doc/oligoHowTo.pdfdirecting
me to the inst/testing directory of VanillaICE where there is
apparently some information on the analysis of 209 CEL files using
VanillaICE, but I am unable to locate the relevant file.

2. If CRLMM is not going to be possible, secondly,
how may I merge the output of SNPRMA, and use it for the same analysis? I
read that the SNPRMA algorithm summarizes the results, but I am unable to
merge the Xba and Hind files as they stand.

> xba.rma <- justSNPRMA(fullFilenames, verbose = TRUE)
> hind.rma <- justSNPRMA(fullFilenames, verbose = TRUE)
> combine(xba.rma,hind.rma)
Error in combine(xba.rma, hind.rma) :
  objects have different annotations: pd.mapping50k.xba240,
pd.mapping50k.hind240
> str(xba.rma)
Formal class 'SnpQSet' [package "oligoClasses"] with 6 slots

Your advice is much appreciated! I am sorry if this seems obvious.

Min-han

/
Min-Han Tan, MBBS, MRCP
Associate Consultant
Department of Medical Oncology
National Cancer Centre
11 Hospital Drive, Singapore 169610
Republic of Singapore
Tel : +65 64368000
Email : tan.min.han@nccs.com.sg

	[[alternative HTML version deleted]]

