Before I or someone else try to tackle this, what does sessionInfo() report when you run your script. /H
2009/6/22 Myriam Peyrard <[email protected]>: > > Dear Henrik, > > I do not get any result, on any chromosomes. But I get all the data in Excel > format in the regions.xls file. Just that it is hard to compile without the > visualisation. I am using the vignette Total Copy Number Analysis (5.0 & > 6.0). Myriam > > Here is my session, from my notes in Tinn-R: > > library(aroma.affymetrix) > library(Biobase) > library(tools) > > chipType <- "GenomeWideSNP_6" > verbose <- Arguments$getVerbose(-8) > timestampOn(verbose) > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") > cdf > gi <- getGenomeInformation(cdf) > gi > si <- getSnpInformation(cdf) > ####################################################################### > #Defining the CEL-set > ####################################################################### > cs <- AffymetrixCelSet$byName("CLP", cdf=cdf) > cs > #AffymetrixCelSet: > #Name: CLP > #Tags: > #Path: rawData/CLP/GenomeWideSNP_6 > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full > #Number of arrays: 28 > #Names: MP01_LKG12, MP02_LKG15, ..., MP28_LKG226 > #Time period: 2009-02-04 21:40:20 -- 2009-03-11 14:10:37 > #Total file size: 1844.47MB > #RAM: 0.02MB > > ####################################################################### > #Calibration for allelic crosstalk > ####################################################################### > acc <- AllelicCrosstalkCalibration(cs) > acc > #AllelicCrosstalkCalibration: > #Data set: CLP > #Input tags: > #User tags: * > #Asterisk ('*') tags: ACC,ra,-XY > #Output tags: ACC,ra,-XY > #Number of files: 28 (1844.47MB) > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full > #Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, > subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr > "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:5] 0.1 0.075 0.05 > 0.03 0.01, ..$ q: num 2, ..$ Q: num 98) > #Output path: probeData/CLP,ACC,ra,-XY/GenomeWideSNP_6 > #Is done: FALSE > #RAM: 0.00MB > > csC <- process(acc, verbose=verbose) > csC > > #AffymetrixCelSet: > #Name: CLP > #Tags: ACC,ra,-XY > #Path: probeData/CLP,ACC,ra,-XY/GenomeWideSNP_6 > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full > #Number of arrays: 28 > #Names: MP01_LKG12, MP02_LKG15, ..., MP28_LKG226 > #Time period: 2009-06-08 11:01:00 -- 2009-06-08 12:51:15 > #Total file size: 1840.64MB > #RAM: 0.02MB > > ####################################################################### > #Summarization > ####################################################################### > plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE, shift=+300) > plm > #AvgCnPlm: > #Data set: CLP > #Chip type: GenomeWideSNP_6,Full > #Input tags: ACC,ra,-XY > #Output tags: ACC,ra,-XY,AVG,+300,A+B > #Parameters: (probeModel: chr "pm"; shift: num 300; flavor: chr "median"; > mergeStrands: logi TRUE; combineAlleles: logi TRUE). > #Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B/GenomeWideSNP_6 > #RAM: 0.00MB > > if (length(findUnitsTodo(plm)) > 0) { > # Fit CN probes quickly (~5-10s/array + some overhead) > units <- fitCnProbes(plm, verbose=verbose) > str(units) > # int [1:945826] 935590 935591 935592 935593 935594 935595 ... > > # Fit remaining units, i.e. SNPs (~5-10min/array) > units <- fit(plm, verbose=verbose) > str(units) > } > > ces <- getChipEffectSet(plm) > ces > #CnChipEffectSet: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B > #Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B/GenomeWideSNP_6 > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full,monocell > #Number of arrays: 28 > #Names: MP01_LKG12, MP02_LKG15, ..., MP28_LKG226 > #Time period: 2009-06-08 15:13:31 -- 2009-06-08 15:13:35 > #Total file size: 754.58MB > #RAM: 0.03MB > #Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > > ####################################################################### > #PCR fragment length normalization > ####################################################################### > fln <- FragmentLengthNormalization(ces) > fln > #FragmentLengthNormalization: > #Data set: CLP > #Input tags: ACC,ra,-XY,AVG,+300,A+B > #User tags: * > #Asterisk ('*') tags: FLN,-XY > #Output tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Number of files: 28 (754.58MB) > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full,monocell > #Algorithm parameters: (subsetToFit: chr "-XY", onMissing: chr "median", > .target: NULL, shift: num 0) > #Output path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6 > #Is done: FALSE > #RAM: 0.00MB > > cesN <- process(fln, verbose=verbose) > #There were 29 warnings (use warnings() to see them) > #> warnings() > #Error: cannot allocate vector of size 14.3 Mb > #In addition: Warning messages: > #1: In attributes(.Data) <- c(attributes(.Data), attrib) : > # Reached total allocation of 1535Mb: see help(memory.size) > #2: In attributes(.Data) <- c(attributes(.Data), attrib) : > # Reached total allocation of 1535Mb: see help(memory.size) > #3: In attributes(.Data) <- c(attributes(.Data), attrib) : > # Reached total allocation of 1535Mb: see help(memory.size) > #4: In attributes(.Data) <- c(attributes(.Data), attrib) : > # Reached total allocation of 1535Mb: see help(memory.size) > > #checking memory allocation, limit of computer and incresing to the max one > can use now. > memory.size() > #[1] 1283.22 > memory.limit(size = NA) > #[1] 2000 > memory.size(max = TRUE) > #[1] 1527.44 > > #RE-DID STEP BEFORE WHERE 29 WARNINGS AND PROBLEM WITH MEMORY > > cesN <- process(fln, verbose=verbose) > #20090609 15:23:58|Normalizing set for PCR fragment-length effects... > #20090609 15:23:59| Already normalized > #20090609 15:23:59| Getting output data set... > #20090609 15:23:59| Getting output data set for > FragmentLengthNormalization... > #20090609 15:23:59| Calling NextMethod: > # List of 6 > # $ generic : chr "getOutputDataSet" > # $ :Classes 'FragmentLengthNormalization', > 'ChipEffectTransform', 'Transform', 'AromaTransform', 'Object' atomic [1:1] > NA > # .. ..- attr(*, ".env")=<environment: 0x0ae9f108> > # .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: > "2009-06-09 09:34:09" > # $ cdf :Classes 'AffymetrixCdfFile', 'UnitNamesFile', > 'AromaChipTypeAnnotationFile', 'AffymetrixFile', 'AromaPlatformInterface', > 'AromaMicroarrayDataFile', 'GenericDataFile', 'Object' atomic [1:1] NA > # .. ..- attr(*, ".env")=<environment: 0x0a0bcc6c> > # .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: > "2009-06-08 15:13:31" > # $ checkChipType : logi FALSE > # $ combineAlleles: logi TRUE > # $ mergeStrands : logi TRUE > #20090609 15:23:59| Getting output data set for > FragmentLengthNormalization... > #20090609 15:23:59| Already retrived. > #20090609 15:23:59| Getting output data set for > FragmentLengthNormalization...done > #20090609 15:23:59| Updating CnChipEffectSet... > #20090609 15:23:59| Scanning for and applying sample annotation files... > #20090609 15:23:59| Defining 0 files... > > #20090609 15:23:59| Defining 0 files...done > #20090609 15:23:59| No sample annotation files found. > #20090609 15:23:59| Scanning for and applying sample annotation > files...done > #20090609 15:23:59| Updating CnChipEffectSet...done > #20090609 15:23:59| Getting output data set for > FragmentLengthNormalization...done > #20090609 15:23:59| Getting output data set...done > #20090609 15:23:59|Normalizing set for PCR fragment-length effects...done > > cesN > #CnChipEffectSet: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6 > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full,monocell > #Number of arrays: 28 > #Names: MP01_LKG12, MP02_LKG15, ..., MP28_LKG226 > #Time period: 2009-06-08 15:13:31 -- 2009-06-08 15:13:35 > #Total file size: 754.58MB > #RAM: 0.03MB > #Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > > ####################################################################### > #Identification of copy-number regions (CNRs) > ####################################################################### > > cbs <- CbsModel(cesN) > #Loading required package: DNAcopy > cbs > #CbsModel: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Chip type (virtual): GenomeWideSNP_6 > #Path: cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6 > #Number of chip types: 1 > #Chip-effect set & reference file pairs: > #Chip type #1 of 1 ('GenomeWideSNP_6'): > #Chip-effect set: > #CnChipEffectSet: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6 > #Platform: Affymetrix > #Chip type: GenomeWideSNP_6,Full,monocell > #Number of arrays: 28 > #Names: MP01_LKG12, MP02_LKG15, ..., MP28_LKG226 > #Time period: 2009-06-08 15:13:31 -- 2009-06-08 15:13:35 > #Total file size: 754.58MB > #RAM: 0.03MB > #Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: > logi TRUE) > #Reference file: > #<average across arrays> > #RAM: 0.00MB > > ####################################################################### > #Fitting copy-number model and displaying results > ####################################################################### > ce <- ChromosomeExplorer(cbs) > ce > #ChromosomeExplorer: > #Name: CLP > #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY > #Number of arrays: 28 > #Path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs > #RAM: 0.00MB > > process(ce, > chromosomes=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23), > verbose=verbose) > > display(ce) > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Henrik Bengtsson > Sent: den 18 juni 2009 18:25 > To: [email protected] > Subject: Re: No CN estimates for SNP 6.0 (Was: Re: [aroma.affymetrix] Re: > CNV analys 28 st SNP 6.0 arrays) > > > Hi, > > are you saying you do not get results from any chromosome? If so, > that's a first very useful clue; if you get from some, something odd > is going odd. Doing CN analysis on these chips is standard procedure, > so it "should work" out of the box. > > In order to help you, what version are you using, i.e. output of > sessionInfo(). Exactly what is script you are using? > > /Henrik > >> -----Original Message----- >> From: Myriam Peyrard >> Sent: den 16 juni 2009 17:01 >> To: 'aroma-affymetrix' >> Subject: RE: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays >> >> I have not gotten any answer about what can be wrong in my Aroma analysis >> when I cannot visualize any CNVs or else on my chromsome maps in >> ChromosomeExplorer. I tried now to run only one chromsome (nr 19) and > again, >> nothing on the plots even for 19. >> I then looked at the Excel file in Cbs named "regions" and there are data > in >> there. So the analysis seems to work but not the visualization. >> What shall I do/try? Is it a computer memory, capacity problem? >> ChromosomeExplorer compatibility? >> >> Myriam > > > On Thu, Jun 11, 2009 at 1:11 AM, Myriam Peyrard<[email protected]> wrote: >> >> Moreover, chrom 1 and 2, in all samples, seems not to have been done, (in >> grey shade when browsing acrross chromosomes and samples. >> Myriam >> >> -----Original Message----- >> From: Myriam Peyrard [mailto:[email protected]] >> Sent: den 11 juni 2009 10:09 >> To: '[email protected]' >> Subject: RE: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays >> Importance: High >> >> OK, nice to hear, about the warnings. >> Then I do: >> display(ce) >> and started to look in my different samples, all chromosomes. >> Seems that there is not a single CNV variation there? >> I did the normalization as non-paired sample sets, with average calculated >> with all samples: >> >> cbs <- CbsModel(cesN) >> >> Is this a normal output? I expected to have many variations and to have to >> sort them out in different ways. Now, I think something has gone wrong >> instead. Any ideas? >> >> Myriam >> >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Henrik Bengtsson >> Sent: den 11 juni 2009 09:38 >> To: [email protected] >> Subject: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays >> >> >> Hi. >> >> On Thu, Jun 11, 2009 at 12:29 AM, Myriam <[email protected]> wrote: >>> >>> Dear all, >>> >>> I have gone through a number of steps in the analysis of 28 arrays of >>> the Genomewide6.0 type and all seems OK until now: >>> >>> #Fitting copy-number model and displaying results >>> ####################################################################### >>> ce <- ChromosomeExplorer(cbs) >>> ce >>> >>> #ChromosomeExplorer: >>> #Name: CLP >>> #Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY >>> #Number of arrays: 28 >>> #Path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs >>> #RAM: 0.00MB >>> >>> process(ce, chromosomes=c >>> (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23), >>> verbose=verbose) >> >> FYI, you can write the above much shorter: >> >> process(ce, chromosomes=1:23, verbose=verbose) >> >>> >>> And the end of the output after many hours run, looks like this: >>> #20090610 02:17:03| Writing CN regions...done >>> #20090610 02:17:03|Generating ChromosomeExplorer report...done >>> #[1] TRUE >>> #There were 50 or more warnings (use warnings() to see the first 50) >>> >>> I am looking at the 50 first warnings and I see that many are of the >>> same type. here comes an example of one of the each category of >>> warning. What shall I do now with each of those? >> >> You don't have to do anything. These warnings are alright and >> expected. No worries here. If you on the other hand get *errors* >> then you have to worry, but those will halt the script immediately. >> >> /Henrik >> >>> 1: In library(package, lib.loc = lib.loc, character.only = >>> TRUE, ... : >>> there is no package called 'Cairo' >>> 2: In method(static, ...) : >>> Ghostscript not found. Searched directories: C:/gs, C:\Program/gs, / >>> gs, C:\Program\Delade filer/gs >>> 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : >>> array has repeated maploc positions >>> >>> 4: In plotDev(pathname, width = width, height = height) : >>> Unable to allocate bitmap >>> 5: In plotDev(pathname, width = width, height = height) : opening >>> device failed >>> 6: In log(theta/thetaRef, base = 2) : NaNs produced >>> 7: In log(theta * thetaRef, base = 2) : NaNs produced >>> 8: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : >>> array has repeated maploc positions >>> >>> Thanks a lot in adavnce for any help! >>> Myriam >>> >>> >>> >>> >>> >>> >>> > >> >> >> >> >> >> > >> > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ 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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