Hi Henrik
I have come across a problem loading Affymetrix 6.0 CEL files using the
AffymetrixCelSet$byName function as described below on a unix 64-bit machine.
Interestingly, the same code has worked before on the same machine with 6.0 CEL
files, and I can load the actual CEL files successfully on a MacBook Pro laptop
using the same code.
the rights for the folders the CEL files are in are:
drwxrwxr-x. 3 johans johans 4096 Oct 6 07:05 GSE19804
drwxrwxr-x. 3 johans johans 4096 Oct 6 21:03 GenomeWideSNP_6
-rwxr-xr-x. 1 johans johans 69104164 Oct 6 20:47 Lung32T.CEL
?
Thanks!
Best regards
Johan
Session info:
library(aroma.affymetrix)
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 v0.5.1 (2011-08-31) 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 v2.2.0 (2011-09-01) 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 v2.2.0 (2011-09-01) successfully loaded. See ?aroma.affymetrix
for help.
> library("ACNE");
Loading required package: MASS
ACNE v0.4.2 (2010-09-28) successfully loaded. See ?ACNE for help.
>
> ####### Read and check that CDFs etc is ok #####
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na26,HB20080821
Full name: GenomeWideSNP_6,Full,na26,HB20080821
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp
File size: 8.97 MB (9407937 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
> acs <- AromaCellSequenceFile$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
> #######
>
>
> data.set.name<-"GSE19804"
> print(paste("doing",data.set.name))
[1] "doing GSE19804"
>
> 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
> cs <- AffymetrixCelSet$byName(data.set.name, cdf=cdf);
> cs <- extract(cs, !isDuplicated(cs))
*** caught segfault ***
address 0x7f449b4b3850, cause 'invalid permissions'
Traceback:
1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
2: readCelHeader(pathname)
3: getHeader.AffymetrixCelFile(this)
4: getHeader(this)
5: getTimestamp.AffymetrixCelFile(X[[19L]], ...)
6: FUN(X[[19L]], ...)
7: base::lapply(this$files, ...)
8: lapply.GenericDataFileSet(this, getTimestamp)
9: lapply(this, getTimestamp)
10: getTimestamps.AffymetrixCelSet(this)
11: getTimestamps(this)
12: isDuplicated.AffymetrixCelSet(cs)
13: isDuplicated(cs)
14: extract.GenericDataFileSet(cs, !isDuplicated(cs))
15: extract(cs, !isDuplicated(cs))
--
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