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 > > > -- > 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to firstname.lastname@example.org > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to email@example.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/