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)) -- 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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