Hi,
remove the temporary file GenomeWideSNP_6,Full,monocell.CDF.tmp in
annotationData/
chipTypes/GenomeWideSNP_6/ and retry. Be patient.
Note that, the first time you process a particular chip type/CDF (here
"GenomeWideSNP_6,Full"), a so called monocell CDF will be created.
This only happens once since that generated file will remain on your
file system. However, it will take quite a while to generate it, e.g.
15-60 minutes depending on your system. What I think happened was
that you gave up while this was happening and interrupted it, or
something else interrupted it.
To create the monocell CDF explicitly, you can do:
library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
cdfM <- getMonocellCdf(cdf, verbose=verbose);
That way, you'll see the progress.
Hope this helps
/Henrik
On Tue, Aug 10, 2010 at 4:59 PM, Vonn <vwal...@email.unc.edu> wrote:
> Hi All,
>
> I'm trying to analyze Affy 6.0 chips by following the steps in the
> vignette for CRMA v 2.0, but I run into problems when I define ces =
> getChipEffectSet(plm). My code, sessionInfo(), traceback(), and R
> output are below. Any thoughts would be greatly appreciated.
>
> Thanks,
>
> Vonn
>
> library(aroma.affymetrix)
> log = verbose = Arguments$getVerbose(-8, timestamp = TRUE)
> options(digits = 4)
> cdf = AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags = "Full")
> print(cdf)
> gi = getGenomeInformation(cdf)
> print(gi)
> si = getSnpInformation(cdf)
> print(si)
> acs = AromaCellSequenceFile$byChipType(getChipType(cdf, fullname =
> FALSE))
> print(acs)
> csR = AffymetrixCelSet$byName("testing", cdf = cdf)
> print(csR)
> acc = AllelicCrosstalkCalibration(csR, model = "CRMAv2")
> print(acc)
> csC = process(acc, verbose = verbose)
> print(csC)
> bpn = BasePositionNormalization(csC, target = "zero")
> print(bpn)
> csN = process(bpn, verbose = verbose)
> print(csN)
> plm = AvgCnPlm(csN, mergeStrands = TRUE, combineAlleles = TRUE)
> fit(plm, verbose = verbose)
> print(plm)
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7
> affxparser_1.18.0
> [4] R.huge_0.2.0 aroma.core_1.7.0
> aroma.light_1.16.1
> [7] matrixStats_0.2.1 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.filesets_0.8.3 digest_0.4.2
> R.utils_1.4.4
> [13] R.oo_1.7.3 R.methodsS3_1.2.0
>
>> traceback()
> 1: print(ces)
>
>> library(aroma.affymetrix)
> Loading required package: R.utils
> Loading required package: R.oo
> Loading required package: R.methodsS3
> R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3
> for help.
> R.oo v1.7.3 (2010-06-04) successfully loaded. See ?R.oo for help.
> R.utils v1.4.4 (2010-07-05) successfully loaded. See ?R.utils for
> help.
> Loading required package: R.filesets
> Loading required package: digest
> R.filesets v0.8.3 (2010-07-06) successfully loaded. See ?R.filesets
> for help.
> Loading required package: aroma.core
> Loading required package: R.cache
> R.cache v0.3.0 (2010-03-13) successfully loaded. See ?R.cache for
> help.
> Loading required package: R.rsp
> R.rsp v0.3.6 (2009-09-16) successfully loaded. See ?R.rsp for help.
> Type browseRsp() to open the RSP main menu in your browser.
> Loading required package: matrixStats
> matrixStats v0.2.1 (2010-04-05) successfully loaded. See ?matrixStats
> for help.
> Loading required package: aroma.light
> aroma.light v1.16.1 (2010-06-23) successfully loaded. See ?aroma.light
> for help.
> aroma.core v1.7.0 (2010-07-26) successfully loaded. See ?aroma.core
> for help.
> Loading required package: aroma.apd
> Loading required package: R.huge
> R.huge v0.2.0 (2009-10-16) successfully loaded. See ?R.huge for help.
> Loading required package: affxparser
> aroma.apd v0.1.7 (2009-10-16) successfully loaded. See ?aroma.apd for
> help.
> aroma.affymetrix v1.7.0 (2010-07-26) successfully loaded. See ?
> aroma.affymetrix for help.
>> log = verbose = Arguments$getVerbose(-8, timestamp = TRUE)
>> options(digits = 4)
>>
>> #Test to make sure things are working
>> cdf = AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags = "Full")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>>
>> gi = getGenomeInformation(cdf)
>> print(gi)
> UgpGenomeInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na30,hg18,HB20100215
> Full name: GenomeWideSNP_6,Full,na30,hg18,HB20100215
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
> File size: 8.97 MB (9407867 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
>>
>> si = getSnpInformation(cdf)
>> print(si)
> UflSnpInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na30,hg18,HB20100215
> Full name: GenomeWideSNP_6,Full,na30,hg18,HB20100215
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
> File size: 7.18 MB (7526452 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
> Number of enzymes: 2
>>
>> acs = AromaCellSequenceFile$byChipType(getChipType(cdf, fullname = FALSE))
>> print(acs)
> AromaCellSequenceFile:
> Name: GenomeWideSNP_6
> Tags: HB20080710
> Full name: GenomeWideSNP_6,HB20080710
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,HB20080710.acs
> File size: 170.92 MB (179217531 bytes)
> RAM: 0.00 MB
> Number of data rows: 6892960
> File format: v1
> Dimensions: 6892960x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: <createdOn>20080710 22:47:02 PDT</
> createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</
> chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</
> filename><filesize>341479928</
> filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></
> srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</
> filename><filesize>96968290</
> filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></
> srcFile2>
> Chip type: GenomeWideSNP_6
> Platform: Affymetrix
>>
>> #Load CEL files in the folder "testing." Note that inside the working
>> directory we have the
>> #path rawData//testing//GenomeWideSNP_6, which contains the appropriate
>> CEL files.
>> csR = AffymetrixCelSet$byName("testing", cdf = cdf)
>> print(csR)
> AffymetrixCelSet:
> Name: testing
> Tags:
> Path: rawData/testing/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Number of arrays: 9
> Names: sample1, sample10, ..., sample9
> Time period: 2010-04-20 13:23:11 -- 2010-04-20 18:43:03
> Total file size: 592.83MB
> RAM: 0.01MB
>> acc = AllelicCrosstalkCalibration(csR, model = "CRMAv2")
>> print(acc)
> AllelicCrosstalkCalibration:
> Data set: testing
> Input tags:
> User tags: *
> Asterisk ('*') tags: ACC,ra,-XY
> Output tags: ACC,ra,-XY
> Number of files: 9 (592.83MB)
> 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 [1:8] 0.1 0.075
> 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
> Output path: probeData/testing,ACC,ra,-XY/GenomeWideSNP_6
> Is done: TRUE
> RAM: 0.00MB
>> csC = process(acc, verbose = verbose)
> 20100810 10:49:37|Calibrating data set for allelic cross talk...
> 20100810 10:49:37| Already calibrated
> 20100810 10:49:37|Calibrating data set for allelic cross talk...done
>> print(csC)
> AffymetrixCelSet:
> Name: testing
> Tags: ACC,ra,-XY
> Path: probeData/testing,ACC,ra,-XY/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Number of arrays: 9
> Names: sample1, sample10, ..., sample9
> Time period: 2010-08-06 14:12:04 -- 2010-08-10 09:38:39
> Total file size: 591.63MB
> RAM: 0.01MB
>> bpn = BasePositionNormalization(csC, target = "zero")
>> print(bpn)
> BasePositionNormalization:
> Data set: testing
> Input tags: ACC,ra,-XY
> User tags: *
> Asterisk ('*') tags: BPN,-XY
> Output tags: ACC,ra,-XY,BPN,-XY
> Number of files: 9 (591.63MB)
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Algorithm parameters: (unitsToFit: chr "-XY", typesToFit: chr "pm",
> unitsToUpdate: NULL, typesToUpdate: chr "pm", shift: num 0, target:
> chr "zero", model: chr "smooth.spline", df: int 5)
> Output path: probeData/testing,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6
> Is done: TRUE
> RAM: 0.00MB
>> csN = process(bpn, verbose = verbose)
> 20100810 10:50:12|Normalization data set for probe-sequence effects...
> 20100810 10:50:12| Already normalized
> 20100810 10:50:12|Normalization data set for probe-sequence
> effects...done
>> plm = AvgCnPlm(csN, mergeStrands = TRUE, combineAlleles = TRUE)
>> fit(plm, verbose = verbose)
> 20100810 10:50:26|Fitting model of class AvgCnPlm...
> AvgCnPlm:
> Data set: testing
> Chip type: GenomeWideSNP_6,Full
> Input tags: ACC,ra,-XY,BPN,-XY
> Output tags: ACC,ra,-XY,BPN,-XY,AVG,A+B
> Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
> "median"; mergeStrands: logi TRUE; combineAlleles: logi TRUE).
> Path: plmData/testing,ACC,ra,-XY,BPN,-XY,AVG,A+B/GenomeWideSNP_6
> RAM: 0.00MB
> 20100810 10:50:26| Identifying non-estimated units...
> 20100810 10:50:26| Getting chip-effect set from data set...
> 20100810 10:50:26| Retrieving monocell CDF...
> 20100810 10:50:26| Monocell chip type:
> GenomeWideSNP_6,Full,monocell
> 20100810 10:50:26| Locating monocell CDF...
> 20100810 10:50:27| Pathname:
> 20100810 10:50:27| Locating monocell CDF...done
> 20100810 10:50:27| Could not locate monocell CDF. Will create one
> for chip type...
> 20100810 10:50:27| Creating monocell CDF...
> 20100810 10:50:27| Chip type: GenomeWideSNP_6,Full
> Error in list(`fit(plm, verbose = verbose)` = <environment>,
> `fit.ProbeLevelModel(plm, verbose = verbose)` = <environment>, :
>
> [2010-08-10 10:50:27] Exception: File already exists: annotationData/
> chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,monocell.CDF.tmp
> at throw(Exception(...))
> at throw.default("File already exists: ", pathname)
> at throw("File already exists: ", pathname)
> at method(static, ...)
> at Arguments$getWritablePathname(tmpDest, mustNotExist = TRUE)
> at createMonocellCdf.AffymetrixCdfFile(this, ..., verbose =
> less(verbose))
> at createMonocellCdf(this, ..., verbose = less(verbose))
> at getMonocellCdf.AffymetrixCdfFile(cdf, ..., verbose =
> less(verbose))
> at getMonocellCdf(cdf, ..., verbose = less(verbose))
> at getChipEffectSet.ProbeLevelModel(this, verbose = verbose)
> at NextMethod("getChipEffectSet", this, ...)
> at getChipEffectSet.SnpPlm(this, verbose = verbose)
> at NextMethod("getChipEffectSet", this, ...)
> at getChipEffectSet.CnPlm(this, verbose = verbose)
> at getChipEffectSet(this, verbose = verbose)
> at findUnitsTodo.ProbeLevelModel(this, verbose = less(verbose)
> 20100810 10:50:27| Creating monocell CDF...done
> 20100810 10:50:27| Could not locate monocell CDF. Will create one
> for chip type...done
> 20100810 10:50:27| Retrieving monocell CDF...done
> 20100810 10:50:27| Getting chip-effect set from data set...done
> 20100810 10:50:27| Identifying non-estimated units...done
> 20100810 10:50:27|Fitting model of class AvgCnPlm...done
>> print(plm)
> AvgCnPlm:
> Data set: testing
> Chip type: GenomeWideSNP_6,Full
> Input tags: ACC,ra,-XY,BPN,-XY
> Output tags: ACC,ra,-XY,BPN,-XY,AVG,A+B
> Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr "median";
> mergeStrands: logi TRUE; combineAlleles: logi TRUE).
> Path: plmData/testing,ACC,ra,-XY,BPN,-XY,AVG,A+B/GenomeWideSNP_6
> RAM: 0.00MB
>> ces = getChipEffectSet(plm)
> Error in list(`getChipEffectSet(plm)` = <environment>,
> `getChipEffectSet.CnPlm(plm)` = <environment>, :
>
> [2010-08-10 10:51:05] Exception: File already exists: annotationData/
> chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,monocell.CDF.tmp
> at throw(Exception(...))
> at throw.default("File already exists: ", pathname)
> at throw("File already exists: ", pathname)
> at method(static, ...)
> at Arguments$getWritablePathname(tmpDest, mustNotExist = TRUE)
> at createMonocellCdf.AffymetrixCdfFile(this, ..., verbose =
> less(verbose))
> at createMonocellCdf(this, ..., verbose = less(verbose))
> at getMonocellCdf.AffymetrixCdfFile(cdf, ..., verbose =
> less(verbose))
> at getMonocellCdf(cdf, ..., verbose = less(verbose))
> at getChipEffectSet.ProbeLevelModel(plm)
> at NextMethod("getChipEffectSet", this, ...)
> at getChipEffectSet.SnpPlm(plm)
> at NextMethod("getChipEffectSet", this, ...)
> at getChipEffectSet.CnPlm(plm)
> at getChipEffectSet(plm)
>> print(ces)
> Error in print(ces) : object 'ces' not found
>
> --
> 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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> 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/
>
--
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/.
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