Hi,
I have run into a problem reading .cel files with aroma.affymetrix. I
am attempting to read in just a single .cel file - this was originally
in binary format (v4), but after downloading the HuEx-1_0-st-v2.cdf
file from the affy website, I realized I would need to convert to
ASCII (v3). I went ahead and did that, but am still getting a cryptic
error. Code follows, with comments interspersed.
> library(aroma.affymetrix)
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3
for help.
R.oo v1.8.1 (2011-07-10) successfully loaded. See ?R.oo for help.
R.utils v1.7.8 (2011-07-24) successfully loaded. See ?R.utils for
help.
Loading required package: R.filesets
Loading required package: digest
R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets
for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.4.3 (2011-07-21) successfully loaded. See ?R.cache for
help.
Attaching package: 'R.cache'
The following object(s) are masked from 'package:R.filesets':
getChecksum
Loading required package: R.rsp
R.rsp v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats
for help.
Loading required package: aroma.light
aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light
for help.
aroma.core v2.1.4 (2011-08-02) successfully loaded. See ?aroma.core
for help.
Attaching package: 'aroma.core'
The following object(s) are masked from 'package:base':
.Machine, append, apply, cat, colMeans, colSums, getOption,
lapply,
library, require, sapply
Loading required package: aroma.apd
Loading required package: R.huge
R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help.
Loading required package: affxparser
aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for
help.
aroma.affymetrix v2.1.6 (2011-07-27) successfully loaded. See ?
aroma.affymetrix for help.
There were 13 warnings (use warnings() to see them)
Package appears to load fine.... Now I read the .cdf file, which is
located in the proper directory:
> cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2.cdf
Filesize: 933.84MB
Chip type: HuEx-1_0-st-v2
RAM: 0.00MB
File format: v3 (text; ASCII)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1432154
Cells per unit: 4.58
Number of QC units: 0
All good up to here. The following performs the troubleshooting steps
to ensure that the data directory structure is correct (direct from
the aroma-affymetrix site):
> library("R.utils");
> pathR <- Arguments$getReadablePath("rawData/", mustExist=TRUE);
> dataSet <- "prostate";
> pathD <- Arguments$getReadablePath(dataSet, path=pathR, mustExist=TRUE);
> chipType <- "HuEx-1_0-st-v2";
> chipTypeS <- gsub(",.*", "", chipType);
> pathDC <- Arguments$getReadablePath(chipTypeS, path=pathD, mustExist=TRUE);
> print(list.files(path=pathDC));
[1] "GSM526134_YX_Exon1_PCA0001.CEL"
Everything appears to be in order. But now, when I try to read the cel
file:
> csR <- AffymetrixCelSet$byName("prostate", cdf=cdf);
Error in list(`AffymetrixCelSet$byName("prostate", cdf = cdf)` =
<environment>, :
[2011-08-10 14:59:25] Exception: Failed to setup a data set for any of
1 data directories located.
at throw(Exception(...))
at throw.default(sprintf("Failed to setup a data set for any of %d
data direct
at throw(sprintf("Failed to setup a data set for any of %d data
directories lo
at method(static, ...)
at AffymetrixCelSet$byName("prostate", cdf = cdf)
I'm baffled by this error message... Here are the results of
print(sessionInfo()):
> print(sessionInfo())
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_2.1.6 affxparser_1.22.1
aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.1.4
[6] aroma.light_1.20.0 matrixStats_0.2.2
R.rsp_0.6.2 R.cache_0.4.3 R.filesets_1.1.0
[11] digest_0.5.0 R.utils_1.7.8
R.oo_1.8.1 R.methodsS3_1.2.1
Any help would be greatly appreciated.
Thanks,
Matt
--
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