I see. Thanks a lot, Sean
On Tue, Aug 6, 2013 at 8:05 PM, Henrik Bengtsson < henrik.bengts...@aroma-project.org> wrote: > Hi. > > On Tue, Aug 6, 2013 at 12:31 PM, ying chen <njs...@gmail.com> wrote: > > Hi Henrik, > > > > > > Sorry I have one more question to bug you. The urls in the df (by df <- > > readDataFrame(db);) point to UCSCgenome browser with NCBI36/hg18 > assembly. I > > looked at the http://www.aroma-project.org/chipTypes/GenomeWideSNP_6page > > resource part, the SNP6 chip type files are listed as based on hg19 > (Human > > Genome build v36.1). This is a typo, right? I thought it should be hg18. > So > > the Cbs out put is also based on hg18, right? > > The genome version ("hg18") in the URLs to the USCC Genome Browser are > (still) hard coded. Please see: > > > https://groups.google.com/d/msg/aroma-affymetrix/r8CtCvdGWnE/jzQFMifxt2MJ > > for more informations/details. > > /Henrik > > > > > Thanks a lot for the help! > > > > Sean > > > > > > > > > > > > > > > > On Fri, Aug 2, 2013 at 11:03 AM, Henrik Bengtsson > > <henrik.bengts...@aroma-project.org> wrote: > >> > >> On Thu, Aug 1, 2013 at 6:37 PM, ying chen <njs...@gmail.com> wrote: > >> > Hi Henrik, > >> > > >> > Thanks a lot for the help. > >> > > >> > For sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"), you mean sm <- > >> > CbsModel(dsT, ref=dfR, tags="HapMapRef"), right? > >> > >> Correct, I meant: > >> > >> sm <- CbsModel(dsT, ref=dfR, tags="HapMapRef") > >> > >> /H > >> > >> > > >> > Thanks, > >> > > >> > Sean > >> > > >> > > >> > > >> > On Thu, Aug 1, 2013 at 6:00 PM, Henrik Bengtsson > >> > <henrik.bengts...@aroma-project.org> wrote: > >> >> > >> >> On Mon, Jul 29, 2013 at 7:45 PM, ying chen <njs...@gmail.com> wrote: > >> >> > Hi Henrik, > >> >> > Thanks a lot for the help! > >> >> > Sorry I have more questions. I am following "How to: Calculate > total > >> >> > copy > >> >> > number ratios from total (non-polymorphic) signals" and "Vignette: > >> >> > Total > >> >> > copy-number segmentation (non-paired CBS)", but I am not sure if I > do > >> >> > it > >> >> > correctly. > >> >> > I have two SNP6 datasets Tumor and HapMap270 and I want to use > >> >> > HpaMap270 > >> >> > as > >> >> > reference to go all the way to CBS step. So I do the following > steps > >> >> > respectively. > >> >> > > ds1 <- doCRMAv2("HapMap270", chipType="GenomeWideSNP_6,Full") > >> >> > > ds2 <- doCRMAv2("Tumor", chipType="GenomeWideSNP_6,Full") > >> >> > After that, I do > >> >> > > dataSet <- "HapMap270" > >> >> > > tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY" > >> >> > > chipType <- "GenomeWideSNP_6" > >> >> > > dsN <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, > >> >> > chipType=chipType) > >> >> > > dataSet <- "Tumor" > >> >> > > tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY" > >> >> > > chipType <- "GenomeWideSNP_6" > >> >> > > dsT <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, > >> >> > chipType=chipType) > >> >> > > dfR <- getAverageFile(dsN) # ? > >> >> > > dsTR <- exportTotalCnRatioSet(dsT, ref=dfR) # ? > >> >> > Would the above two steps work? My question is how to go ahead from > >> >> > here > >> >> > to > >> >> > do CBS and will sm <- CbsModel(dsTR) work? > >> >> > >> >> Skip the exportTotalCnRatioSet() call, and instead use: > >> >> > >> >> sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"); > >> >> > >> >> The 'tags' is just to add an informative tag to the output data set. > >> >> > >> >> /Henrik > >> >> > >> >> > Thanks again for your help! > >> >> > Sean > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > On Sun, Jul 28, 2013 at 4:28 PM, Henrik Bengtsson > >> >> > <henrik.bengts...@aroma-project.org> wrote: > >> >> >> > >> >> >> Hi. > >> >> >> > >> >> >> On Fri, Jul 26, 2013 at 8:02 AM, sean nj <njs...@gmail.com> > wrote: > >> >> >> > Hi guys, > >> >> >> > > >> >> >> > I have a question regarding how to calculate raw copy numbers > >> >> >> > using > >> >> >> > common > >> >> >> > reference instead of average of all samples of the study. > >> >> >> > Basically I > >> >> >> > want > >> >> >> > to use average of HapMap270 samples as reference for all further > >> >> >> > copy > >> >> >> > number > >> >> >> > calculations. > >> >> >> > > >> >> >> > I have a bunch HapMap270 snp6 cel files and I followed Vignette: > >> >> >> > Estimation > >> >> >> > of total copy numbers using the CRMA v2 method (10K-CytoScanHD) > to > >> >> >> > Step > >> >> >> > 5 - > >> >> >> > Calculation of raw copy numbers, and generated ceR and saved it > as > >> >> >> > a > >> >> >> > RData > >> >> >> > file ceR.Rdata. > >> >> >> > >> >> >> It's important to understand that almost all objects in the Aroma > >> >> >> framework are basically "pointers" to external files. For > instance, > >> >> >> your 'ceR', which I assume you've got from something like ceR <- > >> >> >> getAverageFile(ces), is referring to the file with pathname > >> >> >> getPathname(ceR). More below... > >> >> >> > >> >> >> > > >> >> >> > My first question is, how to use this data for any future copy > >> >> >> > number > >> >> >> > analysis? My guess is that instead of calculating the ceR from > the > >> >> >> > sample > >> >> >> > set I can just load the ceR.RData file I saved and use it. > Right? > >> >> >> > >> >> >> First of all, please note that when do ceR <- getAverageFile(ces) > on > >> >> >> the same data set 'ces', the result is already available on file > and > >> >> >> it will be quickly found and returned. In other words, it will > not > >> >> >> recalcuate the averages again [unless you do ceR <- > >> >> >> getAverageFile(ces, force=TRUE)]. > >> >> >> > >> >> >> However, I do understand that you may not want to have to keep a > >> >> >> large > >> >> >> 'ces' data set around, when you're only interested in the pooled > >> >> >> average. In that case, I would copy the file containing the > >> >> >> "average" > >> >> >> to a new data set. Currently, this is not straightforward in > Aroma > >> >> >> (I'll think about something), but you can do the following: > >> >> >> > >> >> >> # Calculate the pooled average > >> >> >> > ceR <- getAverageFile(cesN); > >> >> >> > >> >> >> # Copy this file to plmData/HapMap270,pooled/GenomeWideSNP_6/, > e.g. > >> >> >> > filename <- getFilename(ceR); > >> >> >> > filename > >> >> >> [1] > >> >> >> > >> >> >> > ".average-intensities-median-mad,d03faaf8b707a97c4e43381b1a5d1ef2.CEL" > >> >> >> > rootPath <- getParent(getPath(cesN), depth=2L); > >> >> >> > dataSet <- "HapMap270,pooled"; > >> >> >> > chipType <- getChipType(ceR, fullname=FALSE); > >> >> >> > path <- file.path(rootPath, dataSet, chipType); > >> >> >> > path > >> >> >> [1] "plmData/HapMap270,pooled/GenomeWideSNP_6" > >> >> >> > mkdirs(path); > >> >> >> > copyFile(getPathname(ceR), file.path(path, filename)); > >> >> >> > >> >> >> With this done, you can then grab this pooled reference as: > >> >> >> > >> >> >> > library("aroma.affymetrix") > >> >> >> > path <- "plmData/HapMap270,pooled/GenomeWideSNP_6"; > >> >> >> > filename <- > >> >> >> > > >> >> >> > > >> >> >> > > ".average-intensities-median-mad,d03faaf8b707a97c4e43381b1a5d1ef2.CEL"; > >> >> >> > ceR <- CnChipEffectFile(filename, path=path); > >> >> >> > >> >> >> Note, when you save 'ceR', you are basically saving the reference > to > >> >> >> the file. Yes, you can load it later, but make sure not to move > it, > >> >> >> otherwise you'll get some type of "file not found" error. > >> >> >> > >> >> >> > saveObject(ceR, "HapMap270,GenomeWideSNP_6,reference.Rdata"); > >> >> >> > >> >> >> If already saved, and file not moved, you can then do: > >> >> >> > >> >> >> > library("aroma.affymetrix"); > >> >> >> > ceR <- loadObject("HapMap270,GenomeWideSNP_6,reference.Rdata"); > >> >> >> > >> >> >> All this is very ad hoc (=non-aroma style), and as I said, I'll > see > >> >> >> if > >> >> >> I can come up with a cleaner solution for storing and retrieving > >> >> >> pooled averages. > >> >> >> > >> >> >> > > >> >> >> > My second question is, how to go ahead from there to calculate > the > >> >> >> > relative > >> >> >> > copy numbers for all unit from all samples? The two examples > given > >> >> >> > in > >> >> >> > the > >> >> >> > Vignette are for one unit from one sample and for a few unit on > >> >> >> > chromosome 2 > >> >> >> > for one sample. What is the function to retrieve all units on > all > >> >> >> > chromosomes instead of units <- getUnitsOnChromosome(gi, > >> >> >> > chromosome=2, > >> >> >> > region=c(81,86)*1e6)? > >> >> >> > >> >> >> You can set 'units' to NULL to retrieve all loci, i.e. no need to > >> >> >> use > >> >> >> getUnitsOnChromosome(). FYI, units <- NULL will give the same > data > >> >> >> as > >> >> >> with units <- 1:nbrOfUnits(gi). > >> >> >> > >> >> >> > And what is the function to retrieve all samples > >> >> >> > instead of ce <- getFile(cesN, indexOf(cesN, "NA06985"))? > >> >> >> > >> >> >> Hmm... not clear what you mean. All samples are in 'cesN', and > you > >> >> >> do > >> >> >> need to iterate over them somehow. Is this what you're looking > for? > >> >> >> > >> >> >> for (ii in seq_along(cesN)) { > >> >> >> ce <- getFile(cesN, ii) > >> >> >> ... > >> >> >> } > >> >> >> > >> >> >> Or are you asking how to extract the data from all samples? Then > >> >> >> you > >> >> >> can > >> >> >> do: > >> >> >> > >> >> >> theta <- extractTheta(cesN, units=units) > >> >> >> > >> >> >> but be careful because that loads a lot of data into memory. > >> >> >> > >> >> >> Hope this helps, > >> >> >> > >> >> >> Henrik > >> >> >> > >> >> >> > > >> >> >> > Thanks a lot for the help, > >> >> >> > > >> >> >> > Sean > >> >> >> > > >> >> >> > -- > >> >> >> > -- > >> >> >> > 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 > >> >> >> > aroma-affymetrix@googlegroups.com 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