Hello,
I'm just getting started with aroma.affymetrix, and I'm having difficulty
loading a CEL file into an AffymetrixCelSet. Here is what I am doing:
R version 3.0.1 (2013-05-16) -- "Good Sport"
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> library("aroma.affymetrix");
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.4.4 (2013-05-19) successfully loaded. See ?R.methodsS3 for
help.
R.oo v1.15.0 (2013-08-23) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:methods':
getClasses, getMethods
The following object is masked from 'package:base':
attach, detach, gc, load, save
R.utils v1.26.2 (2013-07-30) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following object is masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, parse, warnings
Loading required package: aroma.core
Loading required package: R.filesets
R.filesets v2.1.0 (2013-08-01) successfully loaded. See ?R.filesets for
help.
Attaching package: 'R.filesets'
The following object is masked from 'package:base':
append, readLines
Loading required package: R.devices
R.devices v2.5.0 (2013-07-30) successfully loaded. See ?R.devices for help.
aroma.core v2.10.1 (2013-08-03) successfully loaded. See ?aroma.core for
help.
Attaching package: 'aroma.core'
The following object is masked from 'package:base':
.Machine, append, apply, colMeans, colSums, library, require, write
Loading required package: aroma.light
Loading required package: matrixStats
matrixStats v0.8.5 (2013-05-25) successfully loaded. See ?matrixStats for
help.
Attaching package: 'matrixStats'
The following object is masked from 'package:aroma.core':
colMedians
aroma.light v1.30.2 (2013-05-20) successfully loaded. See ?aroma.light for
help.
Attaching package: 'aroma.light'
The following objects are masked from 'package:aroma.affymetrix':
averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
plotXYCurve
The following object is masked from 'package:aroma.core':
callNaiveGenotypes, normalizeTumorBoost
Loading required package: affxparser
Attaching package: 'affxparser'
The following object is masked from 'package:aroma.affymetrix':
writeCdf
The following object is masked from 'package:R.utils':
findFiles
The following object is masked _by_ package:aroma.affymetrix:
writeCdf
The following object is masked from package:R.utils:
findFiles
aroma.affymetrix v2.10.0 (2013-08-04) successfully loaded. See
?aroma.affymetrix for help.
Attaching package: 'aroma.affymetrix'
The following objects are masked _by_ 'package:aroma.light':
averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
plotXYCurve
The following object is masked from 'package:affxparser':
writeCdf
The following object is masked from 'package:base':
append, apply, colMeans, colSums, library, require
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> cel_set_raw <- AffymetrixCelSet$byName("snp6_testing", cdf=cdf);
[2013-09-11 16:28:04] Exception: Failed to setup a data set for any of 1
data directories located. The following reasons were reported: (1) a
character vector argument expected (while trying
'rawData/snp6_testing/GenomeWideSNP_6').
at #03. byName.AffymetrixCelSet(static, ...)
- byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'
at #02. byName(static, ...)
- byName() is in environment 'R.filesets'
- originating from '<text>'
at #01. AffymetrixCelSet$byName("snp6_testing", cdf = cdf)
- AffymetrixCelSet$byName() is local of the calling function
Error: Failed to setup a data set for any of 1 data directories located.
The following reasons were reported: (1) a character vector argument
expected (while trying 'rawData/snp6_testing/GenomeWideSNP_6').
Here is my sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_1.30.2 matrixStats_0.8.5 aroma.affymetrix_2.10.0
[4] affxparser_1.32.3 aroma.core_2.10.1 R.devices_2.5.0
[7] R.filesets_2.1.0 R.utils_1.26.2 R.oo_1.15.0
[10] R.methodsS3_1.4.4
loaded via a namespace (and not attached):
[1] PSCBS_0.35.6 R.cache_0.7.1 R.huge_0.5.0 R.rsp_0.9.17
[5] aroma.apd_0.3.0 digest_0.6.3 tools_3.0.1
I think I've set up the directory structure correctly. I can successfully
make an AffymetrixCelSet of an empty dataSet directory, and I get a
different error if I ask for a dataSet that doesn't exist. I've checked my
CDF file and it is not a plain text file.
What's causing this error? As far as I can tell, I'm passing the same types
of arguments as used in <http://www.aroma-project.org/vignettes/CRMAv2>. Is
there somewhere I was supposed to pass a character vector when I didn't?
Thanks,
-Adam Novak
UCSC Bioinformatics Ph.D. Student
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