Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Hi. On Thu, Oct 6, 2011 at 2:36 PM, Johan Staaf johan.st...@med.lu.se wrote: Hi Henrik I have come across a problem loading Affymetrix 6.0 CEL files using the AffymetrixCelSet$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$byChipType(getChipType(cdf, fullname=FALSE)) print(acs) AromaCellSequenceFile: Name: GenomeWideSNP_6 Tags: HB20080710 Full name: GenomeWideSNP_6,HB20080710 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs File size: 170.92 MB (179217531 bytes) RAM: 0.00 MB Number of data rows: 6892960 File format: v1 Dimensions: 6892960x26 Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 Footer: createdOn20080710 22:47:02 PDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6/chipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/filenamefilesize341479928/filesizechecksum2037c033c09fd8f7c06bd042a77aef15/checksum/srcFilesrcFile2filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize96968290/filesizechecksum3dc2d3178f5eafdbea9c8b6eca88a89c/checksum/srcFile2 Chip type: GenomeWideSNP_6 Platform: Affymetrix ### data.set.name-GSE19804 print(paste(doing,data.set.name)) [1] doing GSE19804 cdf AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.cdf Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 cs - AffymetrixCelSet$byName(data.set.name, cdf=cdf); cs - extract(cs, !isDuplicated(cs)) *** caught segfault *** address 0x7f449b4b3850, cause 'invalid permissions'
Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 cs - AffymetrixCelSet$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$files, ...) 8: lapply.GenericDataFileSet(this, getTimestamp) 9: lapply(this, getTimestamp) 10: getTimestamps.AffymetrixCelSet(this) 11: getTimestamps(this) 12: isDuplicated.AffymetrixCelSet(cs) 13: isDuplicated(cs) 14: extract.GenericDataFileSet(cs, !isDuplicated(cs)) 15: extract(cs, !isDuplicated(cs)) Från: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com] f#246;r Henrik Bengtsson [henrik.bengts...@aroma-project.org] Skickat: den 6 oktober 2011 23:43 Till: aroma-affymetrix@googlegroups.com Ämne: Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName 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
