Dear aroma users/authors,
i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF
values so that i can further use them with the method SOMATICS
(Assie'08).
I have not used from the very beginning the wrapper
ds <- doASCRMAv2("TumorProjekt", chipType="GenomeWideSNP_6");
but did all analysis steps explicitly, actually 2 times: one with
argument combineAlleles=FALSE and one with argument
combineAlleles=TRUE.
As i understand it correctly, if i had object ds i could use ds$fracB
to become BAF.
I did not want to recalculate everything and started following:
dataSet <- "TumorProjekt";
tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";
chipType <- "GenomeWideSNP_6";
ds <- AromaUnitFracBCnBinarySet$byName(dataSet, tags=tags,
chipType=chipType);
dfTxt <- writeDataFrame(ds, columns=c("unitName",
"chromosome","position", "*"));
but become
Exception: None of the data directories exist: totalAndFracBData,
rawCnData, cnData, smoothCnData
What could be the reason for this?
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