Hi, Henrik,

I have some Affymetrix SNP6 data on a resistant cell line model after
compound treatment. I want to do a paired analysis comparing the
resistant cell line data to the parental. To make sure that the
changes I see in the paired analysis is indeed acquired aberrations,
not simply a magnitude change between the resistant and parental, I
also want to analyze the resistant and parental data separately
against a common reference (e.g. Hapmap). So my question is how I can
combine both a paired and an unpaired analysis in aroma affymetrix/cn.

Some codes I have for the paired analysis are as follows:

verbose <- Arguments$getVerbose(-8, timestamp=TRUE);

dataSet = "Resistant_model";
chipType = "GenomeWideSNP_6";
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");

dsC = doCRMAv2(dataSet, cdf=cdf, verbose=verbose);

# paired analysis
idxP <- match("Parental", getNames(dsC));
dsP <- extract(dsC, idxP);

idxR <- match("Resistant", getNames(dsC));
dsR <- extract(dsC, idxR);

cns2 <- CbsModel(dsR,dsP);

ce2 <- ChromosomeExplorer(cns2);

process(ce2, verbose=verbose);

I have also loaded a set of preprocessed Hapmap samples as follows:

ds <- AromaUnitTotalCnBinarySet$byName("SNP6_HAPMAP_FEMALE",

dsRef <- getAverageFile(ds, verbose=verbose);

I was wondering whether there is a way that will allow me to construct
a AromaUnitTotalCnBinarySet consisting of: 1) Resistant, 2) Resistant
and 3) Parental; then compare it to another reference set consisting
of: 1) Parental, 2) Hapmap and 3) Hapmap.

I understand that I can do the paired and unpaired analysis
separately, but I want to generate one ChromsomeExplorer report
consisting both of them so I can easily compare across them visually.
Any help you can provide is much appreciated.


When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
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traceback(), and 3) to post a complete code example.

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