Hi,
I know this exception has been discussed before, but it seems to be
different here:
I follow the instruction on http://aroma-project.org/vignettes/CRMAv2 and run:
library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("MOUSEDIVm520650");
gi <- getGenomeInformation(cdf)
si <- getSnpInformation(cdf)
acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
ufl <- getAromaUflFile(cdf);
csR <- AffymetrixCelSet$byName("MOUSEDIVm520650", cdf=cdf)
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
csC <- process(acc, verbose=verbose)
bpn <- BasePositionNormalization(csC, target="zero")
csN <- process(bpn, verbose=verbose)
acc2 <- AllelicCrosstalkCalibration(csN)
plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
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)
fln <- FragmentLengthNormalization(ces, target="zero")
cesN <- process(fln, verbose=verbose)
Here I get the following text:
)
20100918 12:37:49|Normalizing set for PCR fragment-length effects...
20100918 12:37:50| Identifying SNP and CN units...
types
1 2 5
24 626135 1832538
20100918 12:37:59| subsetToUpdate:
int [1:2458673] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:37:59| Identifying SNP and CN units...done
20100918 12:37:59| Retrieving SNP information annotations...
UflSnpInformation:
Name: MOUSEDIVm520650
Tags: na30,mm9,HB20100603
Full name: MOUSEDIVm520650,na30,mm9,HB20100603
Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,na30,mm9,HB20100603.ufl
File size: 9.38 MB (9835569 bytes)
RAM: 0.00 MB
Chip type: MOUSEDIVm520650
Number of enzymes: 2
20100918 12:38:01| Retrieving SNP information annotations...done
20100918 12:38:02| Identifying the subset used to fit normalization
function(s)...
20100918 12:38:02| Identifying units that are SNP and CN probes...
UflSnpInformation:
Name: MOUSEDIVm520650
Tags: na30,mm9,HB20100603
Full name: MOUSEDIVm520650,na30,mm9,HB20100603
Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,na30,mm9,HB20100603.ufl
File size: 9.38 MB (9835569 bytes)
RAM: 0.00 MB
Chip type: MOUSEDIVm520650
Number of enzymes: 2
20100918 12:38:02| Identifying SNPs and CN probes...
types
1 2 5
24 626135 1832538
20100918 12:38:04| units:
int [1:2458673] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:38:04| Identifying SNPs and CN probes...done
20100918 12:38:04| Identify subset of units from genome information...
20100918 12:38:04| subsetToFit: -XY
UgpGenomeInformation:
Name: MOUSEDIVm520650
Tags: na30,mm9,HB20100603
Full name: MOUSEDIVm520650,na30,mm9,HB20100603
Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,na30,mm9,HB20100603.ugp
File size: 11.72 MB (12294266 bytes)
RAM: 0.00 MB
Chip type: MOUSEDIVm520650
20100918 12:38:08| Units to exclude:
int [1:166803] 331975 331977 331986 332014 332041 332047 332060
332065 332211 332292 ...
20100918 12:38:09| Units to include:
int [1:2291894] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:38:09| Identify subset of units from genome information...done
20100918 12:38:09| Reading fragment lengths...
20100918 12:38:21| Reading fragment lengths...done
20100918 12:38:22| Identifying units that are SNP and CN probes...done
int [1:2291870] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:38:22| Identifying the subset used to fit normalization
function(s)...done
20100918 12:38:22| Shift: 0
20100918 12:38:22| onMissing: median
20100918 12:38:22| Array #1 of 1 ('A846-01')...
V1 V2
Min. : 6 Min. : 6
1st Qu.: 615 1st Qu.: 541
Median : 1147 Median : 998
Mean : 1622 Mean : 1477
3rd Qu.: 2197 3rd Qu.: 2001
Max. : 32767 Max. : 32767
NA's :230751 NA's :230751
int [1:2291870] 1 2 3 4 5 6 7 8 9 10 ...
UflSnpInformation:
Name: MOUSEDIVm520650
Tags: na30,mm9,HB20100603
Full name: MOUSEDIVm520650,na30,mm9,HB20100603
Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650,na30,mm9,HB20100603.ufl
File size: 9.38 MB (9835569 bytes)
RAM: 18.76 MB
Chip type: MOUSEDIVm520650
Number of enzymes: 2
20100918 12:38:35| Setting up predefined target functions...
20100918 12:38:35| Target type: zero
20100918 12:38:35| Setting up predefined target functions...done
20100918 12:38:35| Getting cell matrix map...
'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31
32 33 34 ...
20100918 12:38:47| Getting cell matrix map...done
20100918 12:38:47| Getting theta estimates...
20100918 12:39:11| Thetas:
num [1:2458673, 1] 594 331 1330 1368 4346 ...
num [1:2458673, 1] 594 331 1330 1368 4346 ...
V1
Min. : -786
1st Qu.: 1655
Median : 4013
Mean : 6012
3rd Qu.: 7903
Max. :358009
20100918 12:39:11| Getting theta estimates...done
20100918 12:39:11| Calculating total signals...
20100918 12:39:11| Total thetas:
num [1:2458673] 594 331 1330 1368 4346 ...
20100918 12:39:11| Calculating total signals...done
20100918 12:39:11| Normalizing log2 signals...
20100918 12:39:12| Log2 signals:
num [1:2458673] 9.21 8.37 10.38 10.42 12.09 ...
Error in list(`process(fln, verbose = verbose)` = <environment>,
`process.FragmentLengthNormalization(fln, verbose = verbose)` =
<environment>, :
[2010-09-18 12:39:13] Exception: Cannot fit normalization function to
enzyme, because there are no (finite) data points that are unique to
this enzyme: 1
at throw(Exception(...))
at throw.default("Cannot fit normalization function to enzyme,
because there are no (finite) data points that are unique to this
enzyme: ", ee)
at throw("Cannot fit normalization function to enzyme, because there
are no (finite) data points that are unique to this enzyme: ", ee)
at normalizeFragmentLength.default(y, fragmentLengths = fl,
targetFcns = targetFcns, subsetToFit = subset, onMissing = onMissing,
...)
at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
targetFcns, subsetToFit = subset, onMissing = onMissing, ...)
at process.FragmentLengthNormalization(fln, verbose = verbose)
at process(fln, verbose = verbose)
In addition: Warning message:
In log(c(594.256225585938, 330.582916259766, 1330.1611328125,
1368.40588378906, :
NaNs produced
20100918 12:39:13| Normalizing log2 signals...done
20100918 12:39:13| Array #1 of 1 ('A846-01')...done
20100918 12:39:13|Normalizing set for PCR fragment-length effects...done
In previous threads of this mailing group, the solution is always "fit(plm)".
I attach the output of running
> 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)
+ }
20100918 12:11:14|Estimating single-probe CN units...
20100918 12:11:14| Getting chip-effect set...
20100918 12:11:14| Getting chip-effect set...done
20100918 12:11:14| Identifying CN units...
int [1:1832538] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:11:35| Identifying CN units...done
20100918 12:11:35| Identifying subset to fit...
20100918 12:11:36| Identifying non-fitted units in chip-effect file...
20100918 12:11:36| Pathname:
plmData/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650/A846-01,chipEffects.CEL
20100918 12:11:44| Found indices cached on file
20100918 12:11:44| Reading data for these 2458697 cells...
20100918 12:11:45| Reading data for these 2458697 cells...done
20100918 12:12:35| Looking for stdvs <= 0 indicating non-estimated units:
int [1:2458697] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:12:35| Identifying non-fitted units in chip-effect file...done
int [1:1832538] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:12:35| Identifying subset to fit...done
20100918 12:12:35| Identifying cell indices for CN units...
20100918 12:15:16| Identifying cell indices for CN units...done
20100918 12:15:16| Keeping only single-cell units...
20100918 12:15:22| Single-cell units:
int [1:1832538] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:15:22| Cell indices:
int [1:1832538] 68385 5824749 697943 1528748 304414 3059161 6873217
6489401 5012881 1269214 ...
20100918 12:15:22| Keeping only single-cell units...done
20100918 12:15:22| Identifying cell indices for estimates...
int [1:1832538] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:16:50| Identifying cell indices for estimates...done
20100918 12:16:50| Fitting 1 arrays...
20100918 12:16:50| Array #1 ('A846-01') of 1...
20100918 12:16:50| Reading signals...
num [1:1832538] 594 331 1330 1368 4346 ...
20100918 12:16:56| Reading signals...done
20100918 12:16:56| Transforming signals to estimates...
'data.frame': 1832538 obs. of 4 variables:
$ cell : int 25 26 27 28 29 30 31 32 33 34 ...
$ theta : num 594 331 1330 1368 4346 ...
$ sdTheta : num 1.49e-08 1.49e-08 1.49e-08 1.49e-08 1.49e-08 ...
$ outliers: logi FALSE FALSE FALSE FALSE FALSE FALSE ...
20100918 12:16:57| Transforming signals to estimates...done
20100918 12:16:57| Writing estimates...
20100918 12:16:57| Storing flat data to file...
20100918 12:16:57| Updating file...
20100918 12:17:00| Updating file...done
20100918 12:17:00| Storing flat data to file...done
20100918 12:17:00| Writing estimates...done
20100918 12:17:00| Array #1 ('A846-01') of 1...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 357567 9.6 1690412 45.2 26771665 714.9
Vcells 39849044 304.1 110331015 841.8 137895248 1052.1
20100918 12:17:00| Fitting 1 arrays...done
20100918 12:17:00|Estimating single-probe CN units...done
int [1:1832538] 25 26 27 28 29 30 31 32 33 34 ...
20100918 12:17:00|Fitting model of class AvgCnPlm...
AvgCnPlm:
Data set: MOUSEDIVm520650
Chip type: MOUSEDIVm520650
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/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650
RAM: 0.00MB
20100918 12:17:01| Identifying non-estimated units...
20100918 12:17:01| Identifying non-fitted units in chip-effect file...
20100918 12:17:01| Pathname:
plmData/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650/A846-01,chipEffects.CEL
20100918 12:17:05| Found indices cached on file
20100918 12:17:05| Reading data for these 2458697 cells...
20100918 12:17:06| Reading data for these 2458697 cells...done
20100918 12:17:06| Looking for stdvs <= 0 indicating non-estimated units:
int [1:626159] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:17:06| Identifying non-fitted units in chip-effect file...done
20100918 12:17:06| Identifying non-estimated units...done
20100918 12:17:06| Getting model fit for 626159 units.
20100918 12:17:07| Creating CEL file...
20100918 12:17:07| Chip type: MOUSEDIVm520650
20100918 12:17:07| Pathname:
plmData/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650/probeAffinities.CEL
20100918 12:17:07| Method 'create'...
20100918 12:17:07| Creating an empty temporary CEL file...
20100918 12:17:08| Creating an empty temporary CEL file...done
20100918 12:17:08| Renaming file...
20100918 12:17:08| Renaming file...done
20100918 12:17:08| Method 'create'...done
AffymetrixCelFile:
Name: probeAffinities
Tags:
Full name: probeAffinities
Pathname:
plmData/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650/probeAffinities.CEL
File size: 65.74 MB (68930278 bytes)
RAM: 0.00 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: MOUSEDIVm520650
Timestamp: 2010-09-18 12:17:07
20100918 12:17:08| Creating CEL file...done
20100918 12:17:09| Calculating number of units to fit per chunk...
20100918 12:17:09| RAM scale factor: 1
20100918 12:17:09| Bytes per chunk: 1e+08
20100918 12:17:09| Bytes per unit and array: 500
20100918 12:17:09| Bytes per unit: 500
20100918 12:17:09| Number of units per chunk: 200000
20100918 12:17:09| Number of chunks: 4
20100918 12:17:09| Calculating number of units to fit per chunk...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 365054 9.8 1352329 36.2 26771665 714.9
Vcells 36913159 281.7 110331015 841.8 137895248 1052.1
20100918 12:17:09| Fitting chunk #1 of 4...
20100918 12:17:09| Units:
int [1:200000] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:17:09| Reading probe intensities from 1 arrays...
20100918 12:17:09| Identifying CDF cell indices...
$`AFFX-5Q-123`
$`AFFX-5Q-123`$groups
$`AFFX-5Q-123`$groups$`AFFX-5Q-123`
$`AFFX-5Q-123`$groups$`AFFX-5Q-123`$indices
[1] 3466655 3463975 3461295 3458615 3455935 3453255 3450575
3447895 3445215 3442535 3439855 3437175 3434495 3431815 3429135
3466657 3463977 3461297 3458617 3455937
[21] 3453257 3450577 3447897 3445217 3442537 3439857 3437177
3434497 3431817 3429137
20100918 12:18:57| Identifying CDF cell indices...done
List of 1
$ AFFX-5Q-123:List of 1
..$ AFFX-5Q-123:List of 1
.. ..$ intensities: num [1:30, 1] 1956 1144 1624 2440 1995 ...
20100918 12:19:29| Reading probe intensities from 1 arrays...done
20100918 12:19:29| Fitting probe-level model...
20100918 12:19:29| Calling fitUnit() via lapply
List of 1
$ AFFX-5Q-123:List of 1
..$ AFFX-5Q-123:List of 6
.. ..$ theta : num 5567
.. ..$ sdTheta : num 523
.. ..$ thetaOutliers: logi FALSE
.. ..$ phi : num [1:30] 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ sdPhi : num [1:30] 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ phiOutliers : logi [1:30] FALSE FALSE FALSE FALSE FALSE FALSE ...
20100918 12:20:12| Fitting probe-level model...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2567470 68.6 10354880 276.6 26771665 714.9
Vcells 42013221 320.6 110331015 841.8 137895248 1052.1
20100918 12:20:14| Storing probe-affinity estimates...
20100918 12:20:14| Updating units of CnProbeAffinityFile...
20100918 12:20:14| Units:
int [1:200000] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:20:14| Getting cell indices...
20100918 12:20:14| Probe model: pm
20100918 12:20:14| stratifyBy: pm
20100918 12:20:14| Reading cell indices from CDF file...
20100918 12:20:14| Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.CDF
20100918 12:20:14| Units:
int [1:200000] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:20:14| lapplyInChunks()...
20100918 12:20:14| Number of elements per chunk: 1e+05
20100918 12:20:14| Chunk #1 of 2...
20100918 12:20:14| Elements:
int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
20100918 12:20:14| Querying CDF file...
20100918 12:20:32| Querying CDF file...done
20100918 12:20:33| Restructuring...
20100918 12:20:33| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4768412 127.4 10354880 276.6 26771665 714.9
Vcells 44363788 338.5 110331015 841.8 137895248 1052.1
20100918 12:20:34| Chunk #1 of 2...done
20100918 12:20:34| Chunk #2 of 2...
20100918 12:20:34| Elements:
int [1:100000] 431946 431947 431948 431949 431950 431951
431952 431953 431954 431955 ...
20100918 12:20:34| Querying CDF file...
20100918 12:20:54| Querying CDF file...done
20100918 12:20:55| Restructuring...
20100918 12:20:55| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6968414 186.1 10912624 291.4 26771665 714.9
Vcells 46213789 352.6 110331015 841.8 137895248 1052.1
20100918 12:20:56| Chunk #2 of 2...done
20100918 12:20:56| lapplyInChunks()...done
20100918 12:20:56| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6968305 186.1 10912624 291.4 26771665 714.9
Vcells 45913743 350.3 110331015 841.8 137895248 1052.1
20100918 12:20:57| readUnits.AffymetrixCdfFile(): Updating cache
20100918 12:20:58| Getting cell indices...done
20100918 12:22:35| Updating units...
20100918 12:22:35| Encoding units...
20100918 12:22:45| Encoding units...done
20100918 12:22:55| Updating units...done
20100918 12:22:55| Updating units of CnProbeAffinityFile...done
20100918 12:22:55| Storing probe-affinity estimates...done
20100918 12:22:55| Storing chip-effect estimates...
20100918 12:22:55| Updating chip-effect files...
20100918 12:22:56| getCellIndices.CnChipEffectFile()...
20100918 12:23:02| Returning value cached on file: 102.2MB
20100918 12:23:02| getCellIndices.CnChipEffectFile()...done
20100918 12:23:02| Number of files: 1
20100918 12:23:02| Making sure the files are updated in
lexicographic order...
int 1
20100918 12:23:02| Last array: A846-01,chipEffects
20100918 12:23:02| Making sure the files are updated in
lexicographic order...done
20100918 12:23:02| Array #1 of 1 ('A846-01')...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4570357 122.1 12544667 335.0 26771665 714.9
Vcells 43714564 333.6 110331015 841.8 137895248 1052.1
20100918 12:23:23| Array #1 of 1 ('A846-01')...done
20100918 12:23:23| Updating chip-effect files...done
20100918 12:23:23| Storing chip-effect estimates...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 369659 9.9 10035733 268.0 26771665 714.9
Vcells 36913454 281.7 110331015 841.8 137895248 1052.1
AvgCnPlm:
Data set: MOUSEDIVm520650
Chip type: MOUSEDIVm520650
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/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650
RAM: 0.00MB
20100918 12:23:23| Started: 20100918 12:17:09
20100918 12:23:23| Estimated time left: 13.3min
20100918 12:23:23| ETA: 20100918 12:36:42
20100918 12:23:23| Fitting chunk #1 of 4...done
20100918 12:23:23| Fitting chunk #2 of 4...
20100918 12:23:23| Units:
int [1:200000] 531946 531947 531948 531949 531950 531951 531952
531953 531954 531955 ...
20100918 12:23:23| Reading probe intensities from 1 arrays...
20100918 12:23:23| Identifying CDF cell indices...
$JAX00281152
$JAX00281152$groups
$JAX00281152$groups$G
$JAX00281152$groups$G$indices
[1] 3644847 845953 488675 3095339
$JAX00281152$groups$A
$JAX00281152$groups$A$indices
[1] 3644846 845952 488674 3095338
20100918 12:25:00| Identifying CDF cell indices...done
List of 1
$ JAX00281152:List of 2
..$ G:List of 1
.. ..$ intensities: num [1:4, 1] 11380 14531 27811 28459
..$ A:List of 1
.. ..$ intensities: num [1:4, 1] 1365.8 1042.6 26.9 457.3
20100918 12:25:35| Reading probe intensities from 1 arrays...done
20100918 12:25:35| Fitting probe-level model...
20100918 12:25:35| Calling fitUnit() via lapply
List of 1
$ JAX00281152:List of 1
..$ :List of 6
.. ..$ theta : num 21706
.. ..$ sdTheta : num 4946
.. ..$ thetaOutliers: logi FALSE
.. ..$ phi : num [1:4] 1 1 1 1
.. ..$ sdPhi : num [1:4] 1 1 1 1
.. ..$ phiOutliers : logi [1:4] FALSE FALSE FALSE FALSE
20100918 12:26:17| Fitting probe-level model...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2570119 68.7 10316822 275.5 26771665 714.9
Vcells 41913589 319.8 110331015 841.8 137895248 1052.1
20100918 12:26:18| Storing probe-affinity estimates...
20100918 12:26:18| Updating units of CnProbeAffinityFile...
20100918 12:26:18| Units:
int [1:200000] 531946 531947 531948 531949 531950 531951 531952
531953 531954 531955 ...
20100918 12:26:18| Getting cell indices...
20100918 12:26:18| Probe model: pm
20100918 12:26:18| stratifyBy: pm
20100918 12:26:18| Reading cell indices from CDF file...
20100918 12:26:18| Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.CDF
20100918 12:26:18| Units:
int [1:200000] 531946 531947 531948 531949 531950 531951 531952
531953 531954 531955 ...
20100918 12:26:18| lapplyInChunks()...
20100918 12:26:18| Number of elements per chunk: 1e+05
20100918 12:26:18| Chunk #1 of 2...
20100918 12:26:18| Elements:
int [1:100000] 531946 531947 531948 531949 531950 531951
531952 531953 531954 531955 ...
20100918 12:26:18| Querying CDF file...
20100918 12:26:36| Querying CDF file...done
20100918 12:26:37| Restructuring...
20100918 12:26:37| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4770944 127.4 10316822 275.5 26771665 714.9
Vcells 44264183 337.8 110331015 841.8 137895248 1052.1
20100918 12:26:38| Chunk #1 of 2...done
20100918 12:26:38| Chunk #2 of 2...
20100918 12:26:38| Elements:
int [1:100000] 631946 631947 631948 631949 631950 631951
631952 631953 631954 631955 ...
20100918 12:26:38| Querying CDF file...
20100918 12:26:59| Querying CDF file...done
20100918 12:27:00| Restructuring...
20100918 12:27:00| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6970946 186.2 10872663 290.4 26771665 714.9
Vcells 46114184 351.9 110331015 841.8 137895248 1052.1
20100918 12:27:01| Chunk #2 of 2...done
20100918 12:27:01| lapplyInChunks()...done
20100918 12:27:01| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6970837 186.2 10872663 290.4 26771665 714.9
Vcells 45814138 349.6 110331015 841.8 137895248 1052.1
20100918 12:27:03| readUnits.AffymetrixCdfFile(): Updating cache
20100918 12:27:03| Getting cell indices...done
20100918 12:28:44| Updating units...
20100918 12:28:44| Encoding units...
20100918 12:28:53| Encoding units...done
20100918 12:29:05| Updating units...done
20100918 12:29:05| Updating units of CnProbeAffinityFile...done
20100918 12:29:05| Storing probe-affinity estimates...done
20100918 12:29:05| Storing chip-effect estimates...
20100918 12:29:05| Updating chip-effect files...
20100918 12:29:05| getCellIndices.CnChipEffectFile()...
20100918 12:29:11| Returning value cached on file: 102.2MB
20100918 12:29:11| getCellIndices.CnChipEffectFile()...done
20100918 12:29:11| Number of files: 1
20100918 12:29:11| Making sure the files are updated in
lexicographic order...
int 1
20100918 12:29:11| Last array: A846-01,chipEffects
20100918 12:29:11| Making sure the files are updated in
lexicographic order...done
20100918 12:29:11| Array #1 of 1 ('A846-01')...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4570771 122.1 12499684 333.8 26771665 714.9
Vcells 43614222 332.8 110331015 841.8 137895248 1052.1
20100918 12:29:33| Array #1 of 1 ('A846-01')...done
20100918 12:29:33| Updating chip-effect files...done
20100918 12:29:33| Storing chip-effect estimates...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 370116 9.9 9999747 267.1 26771665 714.9
Vcells 36813589 280.9 110331015 841.8 137895248 1052.1
AvgCnPlm:
Data set: MOUSEDIVm520650
Chip type: MOUSEDIVm520650
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/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650
RAM: 0.00MB
20100918 12:29:34| Started: 20100918 12:17:09
20100918 12:29:34| Estimated time left: 7.0min
20100918 12:29:34| ETA: 20100918 12:36:36
20100918 12:29:34| Fitting chunk #2 of 4...done
20100918 12:29:34| Fitting chunk #3 of 4...
20100918 12:29:34| Units:
int [1:200000] 731946 731947 731948 731949 731950 731951 731952
731953 731954 731955 ...
20100918 12:29:34| Reading probe intensities from 1 arrays...
20100918 12:29:34| Identifying CDF cell indices...
$JAX00114219
$JAX00114219$groups
$JAX00114219$groups$G
$JAX00114219$groups$G$indices
[1] 6777891 122563 6633655 3405961
$JAX00114219$groups$A
$JAX00114219$groups$A$indices
[1] 6777890 122562 6633654 3405960
20100918 12:31:14| Identifying CDF cell indices...done
List of 1
$ JAX00114219:List of 2
..$ G:List of 1
.. ..$ intensities: num [1:4, 1] 2514 5291 2512 1979
..$ A:List of 1
.. ..$ intensities: num [1:4, 1] 858 1466 957 655
20100918 12:31:50| Reading probe intensities from 1 arrays...done
20100918 12:31:50| Fitting probe-level model...
20100918 12:31:50| Calling fitUnit() via lapply
List of 1
$ JAX00114219:List of 1
..$ :List of 6
.. ..$ theta : num 3420
.. ..$ sdTheta : num 310
.. ..$ thetaOutliers: logi FALSE
.. ..$ phi : num [1:4] 1 1 1 1
.. ..$ sdPhi : num [1:4] 1 1 1 1
.. ..$ phiOutliers : logi [1:4] FALSE FALSE FALSE FALSE
20100918 12:32:33| Fitting probe-level model...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2570119 68.7 10281094 274.6 26771665 714.9
Vcells 41813589 319.1 110331015 841.8 137895248 1052.1
20100918 12:32:34| Storing probe-affinity estimates...
20100918 12:32:34| Updating units of CnProbeAffinityFile...
20100918 12:32:34| Units:
int [1:200000] 731946 731947 731948 731949 731950 731951 731952
731953 731954 731955 ...
20100918 12:32:34| Getting cell indices...
20100918 12:32:34| Probe model: pm
20100918 12:32:34| stratifyBy: pm
20100918 12:32:34| Reading cell indices from CDF file...
20100918 12:32:34| Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.CDF
20100918 12:32:34| Units:
int [1:200000] 731946 731947 731948 731949 731950 731951 731952
731953 731954 731955 ...
20100918 12:32:34| lapplyInChunks()...
20100918 12:32:34| Number of elements per chunk: 1e+05
20100918 12:32:34| Chunk #1 of 2...
20100918 12:32:34| Elements:
int [1:100000] 731946 731947 731948 731949 731950 731951
731952 731953 731954 731955 ...
20100918 12:32:34| Querying CDF file...
20100918 12:32:52| Querying CDF file...done
20100918 12:32:53| Restructuring...
20100918 12:32:53| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4770944 127.4 10281094 274.6 26771665 714.9
Vcells 44164183 337.0 110331015 841.8 137895248 1052.1
20100918 12:32:54| Chunk #1 of 2...done
20100918 12:32:54| Chunk #2 of 2...
20100918 12:32:54| Elements:
int [1:100000] 831946 831947 831948 831949 831950 831951
831952 831953 831954 831955 ...
20100918 12:32:54| Querying CDF file...
20100918 12:33:15| Querying CDF file...done
20100918 12:33:17| Restructuring...
20100918 12:33:17| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6970946 186.2 11416905 304.9 26771665 714.9
Vcells 46014184 351.1 110331015 841.8 137895248 1052.1
20100918 12:33:18| Chunk #2 of 2...done
20100918 12:33:18| lapplyInChunks()...done
20100918 12:33:18| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 6970837 186.2 11416905 304.9 26771665 714.9
Vcells 45714138 348.8 110331015 841.8 137895248 1052.1
20100918 12:33:19| readUnits.AffymetrixCdfFile(): Updating cache
20100918 12:33:20| Getting cell indices...done
20100918 12:34:57| Updating units...
20100918 12:34:57| Encoding units...
20100918 12:35:08| Encoding units...done
20100918 12:35:19| Updating units...done
20100918 12:35:19| Updating units of CnProbeAffinityFile...done
20100918 12:35:19| Storing probe-affinity estimates...done
20100918 12:35:19| Storing chip-effect estimates...
20100918 12:35:19| Updating chip-effect files...
20100918 12:35:19| getCellIndices.CnChipEffectFile()...
20100918 12:35:35| Returning value cached on file: 102.2MB
20100918 12:35:35| getCellIndices.CnChipEffectFile()...done
20100918 12:35:35| Number of files: 1
20100918 12:35:35| Making sure the files are updated in
lexicographic order...
int 1
20100918 12:35:35| Last array: A846-01,chipEffects
20100918 12:35:35| Making sure the files are updated in
lexicographic order...done
20100918 12:35:35| Array #1 of 1 ('A846-01')...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 4570771 122.1 12457454 332.7 26771665 714.9
Vcells 43514222 332.0 110331015 841.8 137895248 1052.1
20100918 12:35:59| Array #1 of 1 ('A846-01')...done
20100918 12:35:59| Updating chip-effect files...done
20100918 12:35:59| Storing chip-effect estimates...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 370116 9.9 9965963 266.2 26771665 714.9
Vcells 36713589 280.2 110331015 841.8 137895248 1052.1
AvgCnPlm:
Data set: MOUSEDIVm520650
Chip type: MOUSEDIVm520650
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/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650
RAM: 0.00MB
20100918 12:36:00| Started: 20100918 12:17:09
20100918 12:36:00| Estimated time left: 0.8min
20100918 12:36:00| ETA: 20100918 12:36:49
20100918 12:36:00| Fitting chunk #3 of 4...done
20100918 12:36:00| Fitting chunk #4 of 4...
20100918 12:36:00| Units:
int [1:26159] 931946 931947 931948 931949 931950 931951 931952
931953 931954 931955 ...
20100918 12:36:00| Reading probe intensities from 1 arrays...
20100918 12:36:00| Identifying CDF cell indices...
$JAX00068529
$JAX00068529$groups
$JAX00068529$groups$G
$JAX00068529$groups$G$indices
[1] 1120309 4407697 4727659 409205
$JAX00068529$groups$C
$JAX00068529$groups$C$indices
[1] 1120308 4407696 4727658 409204
20100918 12:36:18| Identifying CDF cell indices...done
List of 1
$ JAX00068529:List of 2
..$ G:List of 1
.. ..$ intensities: num [1:4, 1] 3912 2937 6871 8391
..$ C:List of 1
.. ..$ intensities: num [1:4, 1] 1626 596 642 965
20100918 12:37:16| Reading probe intensities from 1 arrays...done
20100918 12:37:16| Fitting probe-level model...
20100918 12:37:16| Calling fitUnit() via lapply
List of 1
$ JAX00068529:List of 1
..$ :List of 6
.. ..$ theta : num 6526
.. ..$ sdTheta : num 1415
.. ..$ thetaOutliers: logi FALSE
.. ..$ phi : num [1:4] 1 1 1 1
.. ..$ sdPhi : num [1:4] 1 1 1 1
.. ..$ phiOutliers : logi [1:4] FALSE FALSE FALSE FALSE
20100918 12:37:22| Fitting probe-level model...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 658186 17.6 4082056 109.1 26771665 714.9
Vcells 37208447 283.9 110331015 841.8 137895248 1052.1
20100918 12:37:22| Storing probe-affinity estimates...
20100918 12:37:22| Updating units of CnProbeAffinityFile...
20100918 12:37:22| Units:
int [1:26159] 931946 931947 931948 931949 931950 931951 931952
931953 931954 931955 ...
20100918 12:37:22| Getting cell indices...
20100918 12:37:22| Probe model: pm
20100918 12:37:22| stratifyBy: pm
20100918 12:37:22| Reading cell indices from CDF file...
20100918 12:37:22| Pathname:
annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.CDF
20100918 12:37:22| Units:
int [1:26159] 931946 931947 931948 931949 931950 931951 931952
931953 931954 931955 ...
20100918 12:37:22| lapplyInChunks()...
20100918 12:37:22| Number of elements per chunk: 1e+05
20100918 12:37:22| Chunk #1 of 1...
20100918 12:37:22| Elements:
int [1:26159] 931946 931947 931948 931949 931950 931951
931952 931953 931954 931955 ...
20100918 12:37:22| Querying CDF file...
20100918 12:37:27| Querying CDF file...done
20100918 12:37:27| Restructuring...
20100918 12:37:27| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1244935 33.3 4082056 109.1 26771665 714.9
Vcells 37803659 288.5 110331015 841.8 137895248 1052.1
20100918 12:37:27| Chunk #1 of 1...done
20100918 12:37:27| lapplyInChunks()...done
20100918 12:37:27| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1244828 33.3 4082056 109.1 26771665 714.9
Vcells 37738214 288.0 110331015 841.8 137895248 1052.1
20100918 12:37:28| readUnits.AffymetrixCdfFile(): Updating cache
20100918 12:37:28| Getting cell indices...done
20100918 12:37:40| Updating units...
20100918 12:37:40| Encoding units...
20100918 12:37:41| Encoding units...done
20100918 12:37:42| Updating units...done
20100918 12:37:42| Updating units of CnProbeAffinityFile...done
20100918 12:37:42| Storing probe-affinity estimates...done
20100918 12:37:42| Storing chip-effect estimates...
20100918 12:37:42| Updating chip-effect files...
20100918 12:37:42| getCellIndices.CnChipEffectFile()...
20100918 12:37:45| Returning value cached on file: 13.4MB
20100918 12:37:45| getCellIndices.CnChipEffectFile()...done
20100918 12:37:45| Number of files: 1
20100918 12:37:45| Making sure the files are updated in
lexicographic order...
int 1
20100918 12:37:45| Last array: A846-01,chipEffects
20100918 12:37:45| Making sure the files are updated in
lexicographic order...done
20100918 12:37:45| Array #1 of 1 ('A846-01')...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 920113 24.6 3265644 87.3 26771665 714.9
Vcells 37430758 285.6 110331015 841.8 137895248 1052.1
20100918 12:37:48| Array #1 of 1 ('A846-01')...done
20100918 12:37:48| Updating chip-effect files...done
20100918 12:37:48| Storing chip-effect estimates...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 370116 9.9 2612515 69.8 26771665 714.9
Vcells 36526669 278.7 110331015 841.8 137895248 1052.1
AvgCnPlm:
Data set: MOUSEDIVm520650
Chip type: MOUSEDIVm520650
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/MOUSEDIVm520650,ACC,ra,-XY,BPN,-XY,AVG,A+B/MOUSEDIVm520650
RAM: 0.00MB
20100918 12:37:48| Started: 20100918 12:17:09
20100918 12:37:48| Estimated time left: 0.0min
20100918 12:37:48| ETA: 20100918 12:37:48
20100918 12:37:48| Fitting chunk #4 of 4...done
20100918 12:37:48| Total time for all units across all 1 arrays:
1239.79s == 20.66min
20100918 12:37:48| Total time per unit across all 1 arrays: 0.00s/unit
20100918 12:37:48| Total time per unit and array: 1.98ms/unit & array
20100918 12:37:48| Total time for one array (2458697 units): 81.14min = 1.35h
20100918 12:37:48| Total time for complete data set: 81.14min = 1.35h
20100918 12:37:48| Fraction of time spent on different tasks: Fitting:
10.8%, Reading: 39.0%, Writing: 49.7% (of which 16.46% is for
encoding/writing chip-effects), Explicit garbage collection: 0.5%
20100918 12:37:48|Fitting model of class AvgCnPlm...done
int [1:626159] 1 2 3 4 5 6 7 8 9 10 ...
There seem to be no irregularities here. Why will it not proceed with cesN?
Best regards
Leif
--
Leif Schauser, PhD
iNANO, Aarhus University
tel. +45 8942 5530
mob. +45 2338 2364
--
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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