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
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