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_6 page
> 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.
>> >> >> >
>> >> >> >
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>> >> >> >
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>> >> >>
>> >> >> --
>> >> >> --
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>> >> >> latest version of the package, 2) to report the output of
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>> >> >> and
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>> >> >
>> >> > --
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
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>> >> > traceback(), and 3) to post a complete code example.
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>> >>
>> >> --
>> >> --
>> >> 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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>> >
>> > --
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
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>> > traceback(), and 3) to post a complete code example.
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>> --
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>> latest version of the package, 2) to report the output of sessionInfo() and
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