My code, traceback, and sessionInfo are below.
Thanks in advance,
Vonn
#Load aroma
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 v1.5.0 (2010-08-04) 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("smalltesting1", cdf = cdf)
print(csR)
AffymetrixCelSet:
Name: smalltesting1
Tags:
Path: rawData/smalltesting1/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: 592.90MB
RAM: 0.01MB
#Create AffyBatch object for csR
ab = extractAffyBatch(csR)
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Attaching package: 'Biobase'
The following object(s) are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'affy'
The following object(s) are masked from 'package:aroma.light':
plotDensity
The following object(s) are masked _by_ package:Biobase :
.Depends
The following object(s) are masked _by_
package:aroma.affymetrix :
.Depends
The following object(s) are masked _by_ package:aroma.apd :
.Depends
The following object(s) are masked _by_ package:R.huge :
.Depends
The following object(s) are masked _by_ package:aroma.core :
.Depends
The following object(s) are masked _by_ package:aroma.light :
.Depends plotDensity
The following object(s) are masked _by_ package:matrixStats :
.Depends
The following object(s) are masked _by_ package:R.rsp :
.Depends
The following object(s) are masked _by_ package:R.cache :
.Depends
The following object(s) are masked _by_ package:R.filesets :
.Depends
The following object(s) are masked _by_ package:R.utils :
.Depends
The following object(s) are masked _by_ package:R.oo :
.Depends
Loading required package: genomewidesnp6,fullcdf
Warning messages:
1: In fcn(...) : Packages reordered in search path: package:affy
2: In extractAffyBatch.AffymetrixCelSet(csR) :
CDF enviroment package 'genomewidesnp6,fullcdf' not installed. The
'affy' package will later try to download it from Bioconductor and
install it.
#########################
#########################
#####Now for normalization. As per CMRAv2.0, we perform allelic
#####crosstalk calibration and normalization for nucleotide-position
#####probe sequence effects.
#########################
#########################
acc = AllelicCrosstalkCalibration(csR, model = "CRMAv2")
csC = process(acc, verbose = verbose)
20100903 13:35:10|Calibrating data set for allelic cross talk...
20100903 13:35:11| Already calibrated
20100903 13:35:11|Calibrating data set for allelic cross talk...done
bpn = BasePositionNormalization(csC, target = "zero")
csN = process(bpn, verbose = verbose)
20100903 13:35:11|Normalization data set for probe-sequence effects...
20100903 13:35:11| Already normalized
20100903 13:35:11|Normalization data set for probe-sequence
effects...done
#Now repeat the above QC steps based on the normalized data
abN = extractAffyBatch(csN)
Loading required package: genomewidesnp6,fullcdf
Error in read.affybatch(filenames = l$filenames, phenoData = l
$phenoData, :
It appears that the file probeData/smalltesting1,ACC,ra,-XY,BPN,-XY/
GenomeWideSNP_6/sample1.CEL is corrupted.
In addition: Warning message:
In extractAffyBatch.AffymetrixCelSet(csN) :
CDF enviroment package 'genomewidesnp6,fullcdf' not installed. The
'affy' package will later try to download it from Bioconductor and
install it.
traceback()
5: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,
ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio")
4: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
description = l$description, notes = notes, compress =
compress,
rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra =
rm.extra,
verbose = verbose, sd = sd, cdfname = cdfname)
3: ReadAffy(filenames = filenames, sampleNames = sampleNames, ...,
verbose = as.logical(verbose))
2: extractAffyBatch.AffymetrixCelSet(csN)
1: extractAffyBatch(csN)
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] Biobase_2.6.1 aroma.affymetrix_1.7.0
aroma.apd_0.1.7
[4] affxparser_1.18.0 R.huge_0.2.0
aroma.core_1.7.0
[7] aroma.light_1.16.1 matrixStats_0.2.1
R.rsp_0.3.6
[10] R.cache_0.3.0 R.filesets_0.8.3
digest_0.4.2
[13] R.utils_1.5.0 R.oo_1.7.3
affy_1.24.2
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.11.1
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