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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>> >
>> >
>>
>> --
>> --
>> 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
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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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