Ok, looks correct here too. Let's try a shortcut; 1) delete reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ and all its subdirectories. 2) Redo:
process(ce, arrays=1, chromosomes=19, verbose=-20) and report *all* the output generated. 3) Check the PNGs in reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/ /Henrik On Tue, Jun 30, 2009 at 12:05 AM, Myriam Peyrard<myriam.peyr...@ki.se> wrote: > > Here is wat I am getting when I do the adviced steps: > ... > cesN <- process(fln, verbose=verbose); > 20090630 08:54:56|Normalizing set for PCR fragment-length effects... > 20090630 08:54:56| Already normalized > 20090630 08:54:56| Getting output data set... > 20090630 08:54:56| Getting output data set for > FragmentLengthNormalization... > 20090630 08:54:56| Calling NextMethod: > List of 6 > $ generic : chr "getOutputDataSet" > $ :Classes 'FragmentLengthNormalization', > 'ChipEffectTransform', 'Transform', 'AromaTransform', 'Object' atomic [1:1] > NA > .. ..- attr(*, ".env")=<environment: 0x03fdc6fc> > .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: > "2009-06-30 08:54:15" > $ cdf :Classes 'AffymetrixCdfFile', 'UnitNamesFile', > 'AromaChipTypeAnnotationFile', 'AffymetrixFile', 'AromaPlatformInterface', > 'AromaMicroarrayDataFile', 'GenericDataFile', 'Object' atomic [1:1] NA > .. ..- attr(*, ".env")=<environment: 0x03b7f4a8> > .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: > "2009-06-30 08:54:07" > $ checkChipType : logi FALSE > $ combineAlleles: logi TRUE > $ mergeStrands : logi TRUE > 20090630 08:54:56| Getting output data set for > FragmentLengthNormalization... > 20090630 08:54:56| Already retrived. > 20090630 08:54:56| Getting output data set for > FragmentLengthNormalization...done > 20090630 08:54:56| Updating CnChipEffectSet... > 20090630 08:54:56| Scanning for and applying sample annotation files... > 20090630 08:54:56| Defining 0 files... > > 20090630 08:54:56| Defining 0 files...done > 20090630 08:54:56| No sample annotation files found. > 20090630 08:54:56| Scanning for and applying sample annotation > files...done > 20090630 08:54:56| Updating CnChipEffectSet...done > 20090630 08:54:56| Getting output data set for > FragmentLengthNormalization...done > 20090630 08:54:56| Getting output data set...done > 20090630 08:54:56|Normalizing set for PCR fragment-length effects...done > > ceR <- getAverageFile(cesN, verbose=verbose); > 20090630 08:55:01|Retrieving average cell signals across 28 arrays... > 20090630 08:55:01| Creating CEL file to store average signals... > 20090630 08:55:01| Pathname: > plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensi > ties-median-mad,efde1e008fb579a08aa5cda998829722.CEL > 20090630 08:55:01| Creating CEL file... > 20090630 08:55:01| Chip type: GenomeWideSNP_6,Full,monocell > 20090630 08:55:01| Pathname: > plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensi > ties-median-mad,efde1e008fb579a08aa5cda998829722.CEL > 20090630 08:55:01| Returning already existing file. > 20090630 08:55:01| Creating CEL file...done > 20090630 08:55:01| Creating CEL file to store average signals...done > CnChipEffectFile: > Name: .average-intensities-median-mad > Tags: efde1e008fb579a08aa5cda998829722 > Full name: .average-intensities-median-mad,efde1e008fb579a08aa5cda998829722 > Pathname: > plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensi > ties-median-mad,efde1e008fb579a08aa5cda998829722.CEL > File size: 26.95 MB (28258317 bytes) > RAM: 0.01 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: GenomeWideSNP_6,Full,monocell > Timestamp: 2009-06-09 15:53:34 > Parameters: (probeModel: chr "pm", mergeStrands: logi FALSE, > combineAlleles: logi FALSE) > 20090630 08:55:03|Retrieving average cell signals across 28 arrays...done > > > thetaR <- extractMatrix(ceR, drop=TRUE) > > str(thetaR) > num [1:1881415] 4448 1674 6573 9634 776 ... > > print(summary(thetaR)) > Min. 1st Qu. Median Mean 3rd Qu. Max. > -149 3192 4888 5509 7158 72180 > > print(summary(is.finite(thetaR))) > Mode TRUE NA's > logical 1881415 0 > > Does it helps? > MYRIAM > > On Mon, Jun 29, 2009 at 1:17 AM, Myriam Peyrard<myriam.peyr...@ki.se> 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: aroma-affymetrix@googlegroups.com >> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >> Sent: den 29 juni 2009 10:03 >> To: aroma-affymetrix@googlegroups.com >> 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<myriam.peyr...@ki.se> >> 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: aroma-affymetrix@googlegroups.com >>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >>> Sent: den 29 juni 2009 01:12 >>> To: aroma-affymetrix@googlegroups.com >>> 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<myriam.peyr...@ki.se> >> 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: aroma-affymetrix@googlegroups.com >>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >>>> Sent: den 18 juni 2009 18:25 >>>> To: aroma-affymetrix@googlegroups.com >>>> 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<myriam.peyr...@ki.se> >>> 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:myriam.peyr...@ki.se] >>>>> Sent: den 11 juni 2009 10:09 >>>>> To: 'aroma-affymetrix@googlegroups.com' >>>>> 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: aroma-affymetrix@googlegroups.com >>>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik > Bengtsson >>>>> Sent: den 11 juni 2009 09:38 >>>>> To: aroma-affymetrix@googlegroups.com >>>>> Subject: [aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays >>>>> >>>>> >>>>> Hi. >>>>> >>>>> On Thu, Jun 11, 2009 at 12:29 AM, Myriam <myriam.peyr...@ki.se> 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
