Hi.
On Thu, Oct 6, 2011 at 2:36 PM, Johan Staaf <johan.st...@med.lu.se> wrote:
> 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:
Almost, but need to see versions etc of everything (especially R
itself and affxparser), so sessionInfo() please.
/Henrik
>
> 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))
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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