Hi all,

I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
have tumor and normal samples, and now I want to apply an unpaired CBS
model. I know ho to do the paired model, but I'm not sure is this code is
right for the unpaired one:

verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
setOption(aromaSettings, "memory/ram", 500.0)

# Verify that the data set can be located:
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
dataSet <- "CEL_files";
dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
setFullName(dsR, dataSet);

# Using CRMAv2
dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);

dsC <- dsList$total;

# Splitting the dataset in normal-tumor pairs
infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is=TRUE,
#Rows in this file are in the same order as arrays in the aroma dataset.

idxN <- which(infoSamples$type=="Normal");
idxT <- which(infoSamples$type=="Tumor");

dsN <- extract(dsC, idxN);
dsT <- extract(dsC, idxT);

# Circular binary segmentation T vs N: Paired model (first N sample pairs
with first T sample)
cns <- CbsModel(dsT, dsN);
fit(cns, verbose=TRUE);
regDatList <- getRegions(cns);

# Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
CORRECT (cns.unpaired keeps me telling that the reference sample is made of
102 files instead of one!).
avgN <- getAverageFile(dsN);
cns.unpaired <- CbsModel(dsT, avgN);
fit(cns.unpaired, verbose=TRUE);
regDatList.unpaired <- getRegions(cns.unpaired);

Besides that, another doubt I have is how to extract raw total copy numbers
into a tab-delimited file after applying doCRMA. Is this code correct? I
assume these CN values are normalized, aren't they?

dataSet <- "CEL_files";
tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";
chipType <- "GenomeWideSNP_6";
ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position",

If I wanted to extract allele-specific CN is it enough to change

tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";


tags <- "ACC,ra,-XY,BPN,-XY,A+B,FLN,-XY";


Thank you very much for your help!




> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] DNAcopy_1.26.0         aroma.cn_0.5.2         aroma.affymetrix_2.1.0
 [4] aroma.apd_0.1.8        affxparser_1.24.0      R.huge_0.2.2
 [7] aroma.core_2.1.0       aroma.light_1.20.0     matrixStats_0.2.2
[10] R.rsp_0.5.3            R.cache_0.4.2          R.filesets_1.0.1
[13] digest_0.5.0           R.utils_1.7.5          R.oo_1.8.0
[16] R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] tools_2.13.0

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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