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?
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
> >
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