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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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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