Sorry, one more question regarding CBS. During
fit(sm, verbose=-10)
Building tuple of reference sets...
Type of reference: median
No reference available.
Calculating average copy-number signals...
Retrieving average unit signals across 291 arrays...
......
I thought I used HapMap270 data as reference, why here it says no reference
available and uses average instead?
Thanks,
Sean
On Thu, Aug 1, 2013 at 10:56 AM, ying chen <njs...@gmail.com> wrote:
> Sorry, one more question regarding CBS. During
>
> fit(sm, verbose=-10)
> Building tuple of reference sets...
> Type of reference: median
> No reference available.
> Calculating average copy-number signals...
> Retrieving average unit signals across 291 arrays...
> ......
>
>
> On Thu, Aug 1, 2013 at 10:53 AM, ying chen <njs...@gmail.com> wrote:
>
>> Hi Henrik,
>>
>> I tried method I mentioned above. But I got an error message when running
>> fit(sm, verbose=-10).
>>
>>
>>
>> Array #1 ('321T') of 291 on chromosome 1...
>> Error in UseMethod("getChecksum") :
>> no applicable method for 'getChecksum' applied to an object of class
>> "list"
>>
>> What did I do wrong?
>>
>> Thanks a lot for the help!
>>
>> Sean
>>
>>
>> > library(aroma.affymetrix)
>>
>> > dataSet <- "HapMap270"
>> > tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"
>> > chipType <- "GenomeWideSNP_6"
>> > dsN <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
>> chipType=chipType)
>> > dataSet <- "Tumor"
>> > dsT <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
>> chipType=chipType)
>> > dfR <- getAverageFile(dsN)
>> > dsTR <- exportTotalCnRatioSet(dsT, ref=dfR)
>> There were 50 or more warnings (use warnings() to see the first 50)
>> > warnings()
>> Warning messages:
>> 1: In log(C) : NaNs produced
>> 2: In log(C) : NaNs produced
>> 3: In log(C) : NaNs produced
>> ...
>> > print(dsTR)
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: 321T, 322T, 323T, ..., T97 [291]
>> Path (to the first file):
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.72 MB
>> RAM: 0.37MB
>> > print(dsT)
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: 321T, 322T, 323T, ..., T97 [291]
>> Path (to the first file):
>> totalAndFracBData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.64 MB
>> RAM: 0.37MB
>> >
>> > sm <- CbsModel(dsTR)
>> >
>> Loading required package: DNAcopy
>> > print(sm)
>> CbsModel:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired
>> Chip type (virtual): GenomeWideSNP_6
>> Path:
>> cbsData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6
>> Number of chip types: 1
>> Sample & reference file pairs:
>> Chip type #1 ('GenomeWideSNP_6') of 1:
>> Sample data set:
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: 321T, 322T, 323T, ..., T97 [291]
>> Path (to the first file):
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.72 MB
>> RAM: 0.37MB
>> Reference: <median of samples>
>> RAM: 0.00MB
>> >
>> > fit(sm, verbose=-10)
>> Building tuple of reference sets...
>> Type of reference: median
>> No reference available.
>> Calculating average copy-number signals...
>> Retrieving average unit signals across 291 arrays...
>> AromaUnitTotalCnBinaryFile:
>> Name: .average-signals-median-mad
>> Tags: 8143f7733336d59b4c432debaf4bb288
>> Full name: .average-signals-median-mad,8143f7733336d59b4c432debaf4bb288
>> Pathname:
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,8143f7733336d59b4c432debaf4bb288.asb
>> File size: 7.18 MB (7526027 bytes)
>> RAM: 0.00 MB
>> Number of data rows: 1881415
>> File format: v1
>> Dimensions: 1881415x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: <createdOn>20130801 10:20:33
>> EDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcDetails><nbrOfFiles>291</nbrOfFiles><checkSum>60c565ccf6239a081e4162b3328e1ccb</checkSum></srcDetails><params><meanName>median</meanName><sdName>mad</sdName></params>
>> Platform: Affymetrix
>> Chip type: GenomeWideSNP_6,Full
>> Number of units to be updated: 1
>> Processing chunk...
>> chr "Indices in chunk:"
>> int 22933
>> Reading data...
>> Reading data...done
>> Estimating averages and standard deviations...
>> Estimating averages and standard deviations...done
>> Writing estimates...
>> Writing estimates...done
>> Processing chunk...done
>> Retrieving average unit signals across 291 arrays...done
>> Calculating average copy-number signals...done
>> Building tuple of reference sets...done
>> Using reference tuple:
>> AromaUnitTotalCnBinarySetTuple:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Chip types: GenomeWideSNP_6
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: .average-signals-median-mad, .average-signals-median-mad,
>> .average-signals-median-mad, ..., .average-signals-median-mad [291]
>> Path (to the first file):
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.62 MB
>> RAM: 0.37MB
>> RAM: 0.00MB
>> Extract DataFileMatrix...
>> Array: 1
>> Test data sets:
>> AromaUnitTotalCnBinarySetTuple:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Chip types: GenomeWideSNP_6
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: 321T, 322T, 323T, ..., T97 [291]
>> Path (to the first file):
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.72 MB
>> RAM: 0.37MB
>> RAM: 0.00MB
>> Test data files:
>> $`GenomeWideSNP_6,Full`
>> AromaUnitTotalCnBinaryFile:
>> Name: 321T
>> Tags:
>> ref=.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7,log2ratio,total
>> Full name:
>> 321T,ref=.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7,log2ratio,total
>> Pathname:
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/321T,ref=.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7,log2ratio,total.asb
>> File size: 7.18 MB (7526390 bytes)
>> RAM: 0.00 MB
>> Number of data rows: 1881415
>> File format: v1
>> Dimensions: 1881415x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: <createdOn>20130801 10:08:04
>> EDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFiles><srcFile><dataSet>Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</dataSet><fullName>321T,total</fullName><filename>321T,total.asb</filename><checksum>d588ec42546855b2a1fd6e68d7181af5</checksum></srcFile><refFile><dataSet>Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</dataSet><fullName>.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7</fullName><filename>.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7.asb</filename><checksum>8a54b83f1c8856778e47648db09bfda9</checksum></refFile></srcFiles>
>> Platform: Affymetrix
>> Chip type: GenomeWideSNP_6,Full
>>
>> attr(,"class")
>> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
>> [3] "list"
>> Type of reference: median
>> Reference data sets:
>> AromaUnitTotalCnBinarySetTuple:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Chip types: GenomeWideSNP_6
>> AromaUnitTotalCnBinarySet:
>> Name: Tumor
>> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Full name: Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
>> Number of files: 291
>> Names: .average-signals-median-mad, .average-signals-median-mad,
>> .average-signals-median-mad, ..., .average-signals-median-mad [291]
>> Path (to the first file):
>> rawCnData/Tumor,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
>> Total file size: 2088.62 MB
>> RAM: 0.37MB
>> RAM: 0.00MB
>> Extract DataFileMatrix...done
>> Genomic-signal tags:
>> ref=.average-signals-median-mad,899bb16b33895d8872112e64f5eb74b7,log2ratio,total
>> Reference tags: 688d239f3db29d92d513e604879b915d
>> Array #1 ('321T') of 291 on chromosome 1...
>> Error in UseMethod("getChecksum") :
>> no applicable method for 'getChecksum' applied to an object of class
>> "list"
>> Array #1 ('321T') of 291 on chromosome 1...done
>> >
>> >
>> > sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] DNAcopy_1.34.0 aroma.affymetrix_2.9.0 affxparser_1.32.1
>> [4] aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.30.2
>> [7] aroma.core_2.9.0 matrixStats_0.8.1 R.rsp_0.8.2
>> [10] R.devices_2.2.2 R.filesets_2.0.1 R.utils_1.23.2
>> [13] R.oo_1.13.0 R.methodsS3_1.4.4
>>
>> loaded via a namespace (and not attached):
>> [1] digest_0.6.3 PSCBS_0.34.8 R.cache_0.6.5
>> >
>> > traceback()
>> No traceback available
>> >
>>
>>
>>
>>
>>
>> On Mon, Jul 29, 2013 at 10:45 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?
>>> 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
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>>>> > To post to this group, send email to
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>>>> >
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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.
>>>>
>>>>
>>>> You received this message because you are subscribed to the Google
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>>>> To post to this group, send email to aroma-affymetrix@googlegroups.com
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>>>>
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>>>>
>>>>
>>>
>>
>
--
--
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