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 >> > To unsubscribe and other options, go to >> > http://www.aroma-project.org/forum/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to aroma-affymetrix+unsubscr...@googlegroups.com. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> -- >> -- >> 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 >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> >> --- >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to aroma-affymetrix+unsubscr...@googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> > > -- > -- > 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 > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > -- -- 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. 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