Dear Usergrop.
while proccessing data from the 5000k Sty array (but not the Nsp set),
I receive the folleowing error:
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> csC <- process(acc)
Error in sort.list(pairsToBuild) :
'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
Calls: process ... groupBySnpNucleotides.AromaCellSequenceFile -> sort
-> sort.list
In addition: Warning messages:
1: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'idxs' not found
2: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'seqsPP' not found
3: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'positions' not found
4: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'cellsPP' not found
5: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'snpPosition' not found
Execution halted
Any ideas what could be the cause?
Thank you
Karl-Heinz
Session log:
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
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'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Attempting to load the environment '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.
Loading required package: utils
R.oo v1.7.2 (2010-04-13) successfully loaded. See ?R.oo for help.
R.utils v1.4.0 (2010-03-24) successfully loaded. See ?R.utils for help.
[Previously saved workspace restored]
> library("aroma.affymetrix")
Loading required package: R.filesets
Loading required package: digest
R.filesets v0.8.1 (2010-04-22) 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 v1.15.1 (2009-11-01) successfully loaded. See ?aroma.light for help.
aroma.core v1.5.0 (2010-02-22) 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 v1.5.0 (2010-02-22) successfully loaded. See
?aroma.affymetrix for help.
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> options(digits=4) # Don't display too many decimals.
>
> chiptype='Mapping250K_Sty'
> project<-"haprefTrio"
>
> cdf <- AffymetrixCdfFile$byChipType(chiptype)
> cs <- AffymetrixCelSet$byName(project,chipType=chiptype)
> print(cs)
AffymetrixCelSet:
Name: haprefTrio
Tags:
Path: rawData/haprefTrio/Mapping250K_Sty
Platform: Affymetrix
Chip type: Mapping250K_Sty
Number of arrays: 8
Names: NA10851_FinSty_vR2_578246_A1_2_SC1,
NA10855_FinSty_vR2_555824_A4_2_SC1, ...,
NA12234_FinSty_vR2_554144_A12_2_SC2
Time period: 2005-08-31 15:29:36 -- 2005-09-01 15:14:51
Total file size: 501.33MB
RAM: 0.02MB
> gi <- getGenomeInformation(cdf)
> print(gi)
DChipGenomeInformation:
Name: Mapping500K genome info hg17
Tags:
Full name: Mapping500K genome info hg17
Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping500K genome
info hg17.txt
File size: 22.91 MB (24021904 bytes)
RAM: 0.00 MB
Chip type: Mapping250K_Sty
> si <- getSnpInformation(cdf)
20100531 15:51:53|Defining DChipSnpInformation from chip type...
20100531 15:51:53| Chip type: Mapping250K_Sty
20100531 15:51:53| Version:
20100531 15:51:53| Located pathname:
annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty snp info.txt
20100531 15:51:53| Instantiating DChipSnpInformation...
DChipSnpInformation:
Name: Mapping250K_Sty snp info
Tags:
Full name: Mapping250K_Sty snp info
Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty
snp info.txt
File size: 24.23 MB (25402597 bytes)
RAM: 0.00 MB
Chip type: Mapping250K_Sty
Number of enzymes: 1
20100531 15:51:53| Instantiating DChipSnpInformation...done
20100531 15:51:53|Defining DChipSnpInformation from chip type...done
> print(si)
DChipSnpInformation:
Name: Mapping250K_Sty snp info
Tags:
Full name: Mapping250K_Sty snp info
Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty snp info.txt
File size: 24.23 MB (25402597 bytes)
RAM: 0.00 MB
Chip type: Mapping250K_Sty
Number of enzymes: 1
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: Mapping250K_Sty
Tags:
Full name: Mapping250K_Sty,
Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty,.acs
File size: 162.50 MB (170393859 bytes)
RAM: 0.00 MB
Number of data rows: 6553600
File format: v1
Dimensions: 6553600x26
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>20100529 10:27:19
EDT</createdOn><platform>Affymetrix</platform><chipType>Mapping250K_Sty</chipType>
Chip type: Mapping250K_Sty
Platform: Affymetrix
> csR <- AffymetrixCelSet$byName(project, cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: haprefTrio
Tags:
Path: rawData/haprefTrio/Mapping250K_Sty
Platform: Affymetrix
Chip type: Mapping250K_Sty
Number of arrays: 8
Names: NA10851_FinSty_vR2_578246_A1_2_SC1,
NA10855_FinSty_vR2_555824_A4_2_SC1, ...,
NA12234_FinSty_vR2_554144_A12_2_SC2
Time period: 2005-08-31 15:29:36 -- 2005-09-01 15:14:51
Total file size: 501.33MB
RAM: 0.02MB
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> csC <- process(acc)
Error in sort.list(pairsToBuild) :
'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
Calls: process ... groupBySnpNucleotides.AromaCellSequenceFile -> sort
-> sort.list
In addition: Warning messages:
1: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'idxs' not found
2: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'seqsPP' not found
3: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'positions' not found
4: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'cellsPP' not found
5: In rm(idxs, seqsPP, positions, cellsPP, snpPosition, cells, pos) :
object 'snpPosition' not found
Execution halted
>
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7 affxparser_1.18.0
[4] R.huge_0.2.0 aroma.core_1.5.0 aroma.light_1.15.1
[7] matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0
[10] R.filesets_0.8.1 digest_0.4.2 R.utils_1.4.0
[13] R.oo_1.7.2 R.methodsS3_1.2.0
> traceback()
No traceback available
>
rawData/haprefTrio/Mapping250K_Sty:
md5.lst
NA10863_FinSty_vR2_554144_A10_2_SC1.EXP
NA12056_FinSty_vR2_578246_A2_2_SC2.EXP
NA10851_FinSty_vR2_578246_A1_2_SC1.CEL
NA11831_FinSty_vR2_555824_A5_2_SC2.CEL
NA12057_FinSty_vR2_578246_A3_2_SC3.CEL
NA10851_FinSty_vR2_578246_A1_2_SC1.CHP
NA11831_FinSty_vR2_555824_A5_2_SC2.CHP
NA12057_FinSty_vR2_578246_A3_2_SC3.CHP
NA10851_FinSty_vR2_578246_A1_2_SC1.EXP
NA11831_FinSty_vR2_555824_A5_2_SC2.EXP
NA12057_FinSty_vR2_578246_A3_2_SC3.EXP
NA10855_FinSty_vR2_555824_A4_2_SC1.CEL
NA11832_FinSty_vR2_555824_A6_2_SC3.CEL
NA12234_FinSty_vR2_554144_A12_2_SC2.CEL
NA10855_FinSty_vR2_555824_A4_2_SC1.CHP
NA11832_FinSty_vR2_555824_A6_2_SC3.CHP
NA12234_FinSty_vR2_554144_A12_2_SC2.CHP
NA10855_FinSty_vR2_555824_A4_2_SC1.EXP
NA11832_FinSty_vR2_555824_A6_2_SC3.EXP
NA12234_FinSty_vR2_554144_A12_2_SC2.EXP
NA10863_FinSty_vR2_554144_A10_2_SC1.CEL NA12056_FinSty_vR2_578246_A2_2_SC2.CEL
NA10863_FinSty_vR2_554144_A10_2_SC1.CHP NA12056_FinSty_vR2_578246_A2_2_SC2.CHP
annotationData/chipTypes/Mapping250K_Sty:
500K Sty Concordance.xls Mapping250K_Sty genome info
hg17.txt Mapping250K_Sty.psi Mapping500K genome
info hg17.txt
AFFX_README-NetAffx-CSV-Files.txt
Mapping250k_Sty_genome_info_hg18.txt Mapping250K_Sty.SMD
na30
Mapping250K_Sty,.acs Mapping250K_Sty.GRC
Mapping250K_Sty snp info.txt README.probeSeqFormat.txt
Mapping250K_Sty.cdf Mapping250K_Sty.mdl
Mapping250K_Sty.specialSNPs Sty_consensus.txt
Mapping250K_Sty.chrx Mapping250K_Sty.na28.annot.csv
Mapping250K_Sty.txt
Mapping250K_Sty.cif Mapping250K_Sty.probe_tab
Mapping250K_Sty.v1.5.birdseed.models
annotationData/chipTypes/Mapping250K_Sty/na30:
Mapping250K_Sty.na30.annot.csv
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