Ok, more things outruled. Next troublehooting step; what does the following give?
... cesN <- process(fln, verbose=verbose); ceR <- getAverageFile(cesN, verbose=verbose); thetaR <- extractMatrix(ceR, drop=TRUE); str(thetaR); print(summary(thetaR)); print(summary(is.finite(thetaR))); /H On Mon, Jun 29, 2009 at 1:17 AM, Myriam Peyrard<[email protected]> wrote: > I see tons of PNG files but all are empty: just the frame with scale, etc. > But not own array data on them. For the largest chromosome 1 I have 7 output > files (ending with 0001, 0002, 0004, 0008, 0016, 0048, 0064) and for the > smallest chr 21, I have only the first 3 outputs. Seems that I have for all > the 28 arrays I have done. So many files!!! > > I tried to open them amnually and they are as I said above. > > I do use Firefox as internet browser. > Myriam > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Henrik Bengtsson > Sent: den 29 juni 2009 10:03 > To: [email protected] > Subject: [aroma.affymetrix] Re: No plot CNV analysis (Myriam) > > > In directory > > reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/ > > you should see many PNG files. Do they exists? How many are they? > What do you see when you open them "manually"? What internet browser > do you use? > > /Henrik > > On Mon, Jun 29, 2009 at 12:50 AM, Myriam Peyrard<[email protected]> > wrote: >> Thank you Henrik. >> I re-run the whole until fragment normalization in the script I sent you >> before (see below). >> Then did: >> plotDensity(cesN) >> and seeing a nice number of curves, more or less overlapping for my > arrays. >> I attach the output (in 2 different file formats) and may be you can judge >> yourself that it is as it should. >> >> So I have signals as I see density curves. >> I run the analysis on my laptop which allows me to use 1.5 Gb Ram. I have >> ordered one more Gb of memory but will have to wait a few days to get it >> installed. If this is the problem, then I will have to wait end of July to >> try it as I will be gone for 3 weeks from next week. >> >> But as I see data in my Excel regions files, isn´t so that the data is >> produced and just the form of the output is the problem? >> >> Best regards, >> Myriam. >> >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Henrik Bengtsson >> Sent: den 29 juni 2009 01:12 >> To: [email protected] >> Subject: [aroma.affymetrix] Re: No plot CNV analysis (Myriam) >> >> >> Hi, >> >> my initial guess is that the when the fragmentation-length >> normalization failed the first time it somehow generated empty output >> files. To check this, try to plot the FLN normalized signals, e.g. >> >> plotDensity(cesN) >> >> You should see density curves as in >> >> >> > http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy >> -numbers-using-the-crma-v2-method >> >> If not, the signals are probably all zeros. If so, then delete the >> following directory: >> >> plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6 >> >> and retry your script. >> >> Also, you shouldn't run out of memory here unless you have very >> limited RAM. Are you loading a large session image at the start? >> >> Cheers, >> >> /Henrik >> >> On Mon, Jun 22, 2009 at 1:07 AM, Myriam Peyrard<[email protected]> > wrote: >>> >>> 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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