Hi.
On Thu, Oct 14, 2010 at 4:38 AM, allab <asphod...@googlemail.com> wrote:
> 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.
If you wish to get allele B fractions (BAFs) you need
combineAlleles=FALSE, which is the default of doASCRMAv2().
>
> As i understand it correctly, if i had object ds i could use ds$fracB
> to become BAF.
Correct. The 'ds' object is actually an R list containing two data
set elements: 'total' and 'fracB'. You are interested in the latter
here.
> I did not want to recalculate everything and started following:
FYI, the key thing with the aroma framework is that it will *not*
recalculate already processed data; your results are persistent across
R sessions since they are stored on the file system. Sure, if you
redo doASCRMAv2() there will be some overhead, but most steps are
skipped.
However, it is true that you can also load the data sets as you try next:
>
> dataSet <- "TumorProjekt";
> tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";
> chipType <- "GenomeWideSNP_6";
> ds <- AromaUnitFracBCnBinarySet$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?
So the error occur in the ds <- AromaUnitFracBCnBinarySet$byName(...)
step. The writeDataFrame() step is not part of this. (Please try to
paste the error where it belongs/as it occurs). The error says that
it cannot find the data set you are asking it to load (in any of the
so called root directories totalAndFracBData/, rawCnData/, cnData/,
smoothCnData/ in the current directory). The key to get this right is
that you are in the same working directory as you were when you did
doASCRMAv2(); from the error message it looks like you are in a
different working directory because it cannot find any of the reported
directories and it should find totalAndFracBData/.
You also have to make sure you are using exactly the same data set
name and tags. It should match what:
dsList <- doASCRMAv2("TumorProjekt", chipType="GenomeWideSNP_6");
print(dsList);
outputs, especially what print(dsList$fracB) reports.
Hope this helps
/Henrik
>
>
> --
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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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