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 >>>> 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.