Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name
Hello Henrik, here is my script basedir - Projects/DrugRep/GEOData/ srcdir = paste(basedir,AZD2,sep=) workdir = paste(basedir,Workdir,sep=) setwd(workdir) tarFile-paste(basedir,AZD2/GSE4757_RAW.tar,sep=) covdesc - paste(basedir,AZD2/GSE4757.covdesc,sep=) convertCdf(annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf, annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,bin.cdf) gsedir- strsplit(basename(tarFile),'_')[[1]][1] print(paste(Untarring,tarFile)) write(paste(Untarring,tarFile), file=test.log, append = TRUE) # create a rawdata folder # create annotationData Folder dir.create(rawData,recursive=TRUE) #dir.create(annotationData,recursive=TRUE) # get annotation chip file if it does not exist in local folder chipType - HG-U133_Plus_2 datafolder - paste(rawData/,gsedir,/,chipType,sep=) dir.create(datafolder , recursive=TRUE) untar(tarFile,exdir=datafolder) # Gunzip all the cel files setwd(datafolder) getwd() celfiles - list.files(pattern=CEL.gz,ignore.case = TRUE) lapply(celfiles,gunzip) # Create Cdf object setwd(../../..) cdf - AffymetrixCdfFile$byChipType(chipType); cs - AffymetrixCelSet$byName(gsedir, cdf=cdf); # gcRMA background correction bc - GcRmaBackgroundCorrection(cs); #this is where it errors ## csB - process(bc); # RMA quantile normalization qn - QuantileNormalization(csB, typesToUpdate=pm); csN - process(qn); # RMA probe summarization plm - RmaPlm(csN, flavor=oligo); fit(plm); # Extract chip effects on the log2 scale ces - getChipEffectSet(plm); theta - extractMatrix(ces); rownames(theta) - getUnitNames(cdf); theta - log2(theta); and here is my session info sessionInfo(); R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.6.0 affxparser_1.30.0 aroma.apd_0.2.3 [4] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.6.0 [7] matrixStats_0.5.3 R.rsp_0.8.2R.cache_0.6.3 [10] R.devices_2.1.1R.filesets_1.1.5 digest_0.5.2 [13] R.utils_1.18.0 R.oo_1.10.1R.methodsS3_1.4.2 [16] e1071_1.6-1class_7.3-5 thanks, rajesh On Monday, November 19, 2012 11:04:15 AM UTC+5:30, Henrik Bengtsson wrote: Hi, I've never seen that before, but remove any *.tmp or *.tmp.tmp etc files and try again. If that does not work, then please 1. show your script exactly at it is, 2. show the output you get from library(aroma.affymetrix); sessionInfo(); /Henrik. On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpa...@gmail.comjavascript: wrote: Thanks Much Henrik. I used the ACS file, but I am not able to go further than the process(). I am getting an error Error: Failed to rename temporary file: probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp - probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp In addition: Warning messages: 1: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason 'Permission denied' 2: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36', reason 'Permission denied' 3: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf', reason 'Permission denied' 4: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d', reason 'Permission denied' Thanks, Rajesh. On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote: Hello All, I am getting the following error when doing process in aroma: csB - process(bc,verbose=TRUE); Background correcting data set... Computing probe affinities (independent of data)... [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = verbose) - getProbeSequenceData.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #08. getProbeSequenceData(this, safe = safe, verbose = verbose) - getProbeSequenceData() is in environment 'aroma.affymetrix' at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., verbose = less(verbose)) - computeAffinities.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #06. computeAffinities(cdf, paths = probePath, ..., verbose =
Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name
Did you retry by first remove any of those *.tmp or *.tmp.tmp etc and rerunning dataSet - GSE4757,OBC; chipType - HG-U133_Plus_2; cdf - AffymetrixCdfFile$byChipType(chipType); cs - AffymetrixCelSet$byName(dataSet, cdf=cdf); print(cs); bc - GcRmaBackgroundCorrection(cs); print(bc); csB - process(bc); print(csB); ? /Henrik On Mon, Nov 19, 2012 at 1:27 AM, Raj Patrao rlpat...@gmail.com wrote: Hello Henrik, here is my script basedir - Projects/DrugRep/GEOData/ srcdir = paste(basedir,AZD2,sep=) workdir = paste(basedir,Workdir,sep=) setwd(workdir) tarFile-paste(basedir,AZD2/GSE4757_RAW.tar,sep=) covdesc - paste(basedir,AZD2/GSE4757.covdesc,sep=) convertCdf(annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf, annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,bin.cdf) gsedir- strsplit(basename(tarFile),'_')[[1]][1] print(paste(Untarring,tarFile)) write(paste(Untarring,tarFile), file=test.log, append = TRUE) # create a rawdata folder # create annotationData Folder dir.create(rawData,recursive=TRUE) #dir.create(annotationData,recursive=TRUE) # get annotation chip file if it does not exist in local folder chipType - HG-U133_Plus_2 datafolder - paste(rawData/,gsedir,/,chipType,sep=) dir.create(datafolder , recursive=TRUE) untar(tarFile,exdir=datafolder) # Gunzip all the cel files setwd(datafolder) getwd() celfiles - list.files(pattern=CEL.gz,ignore.case = TRUE) lapply(celfiles,gunzip) # Create Cdf object setwd(../../..) cdf - AffymetrixCdfFile$byChipType(chipType); cs - AffymetrixCelSet$byName(gsedir, cdf=cdf); # gcRMA background correction bc - GcRmaBackgroundCorrection(cs); #this is where it errors ## csB - process(bc); # RMA quantile normalization qn - QuantileNormalization(csB, typesToUpdate=pm); csN - process(qn); # RMA probe summarization plm - RmaPlm(csN, flavor=oligo); fit(plm); # Extract chip effects on the log2 scale ces - getChipEffectSet(plm); theta - extractMatrix(ces); rownames(theta) - getUnitNames(cdf); theta - log2(theta); and here is my session info sessionInfo(); R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.6.0 affxparser_1.30.0 aroma.apd_0.2.3 [4] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.6.0 [7] matrixStats_0.5.3 R.rsp_0.8.2R.cache_0.6.3 [10] R.devices_2.1.1R.filesets_1.1.5 digest_0.5.2 [13] R.utils_1.18.0 R.oo_1.10.1R.methodsS3_1.4.2 [16] e1071_1.6-1class_7.3-5 thanks, rajesh On Monday, November 19, 2012 11:04:15 AM UTC+5:30, Henrik Bengtsson wrote: Hi, I've never seen that before, but remove any *.tmp or *.tmp.tmp etc files and try again. If that does not work, then please 1. show your script exactly at it is, 2. show the output you get from library(aroma.affymetrix); sessionInfo(); /Henrik. On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpa...@gmail.com wrote: Thanks Much Henrik. I used the ACS file, but I am not able to go further than the process(). I am getting an error Error: Failed to rename temporary file: probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp - probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp In addition: Warning messages: 1: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason 'Permission denied' 2: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36', reason 'Permission denied' 3: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf', reason 'Permission denied' 4: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d', reason 'Permission denied' Thanks, Rajesh. On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote: Hello All, I am getting the following error when doing process in aroma: csB - process(bc,verbose=TRUE); Background correcting data set... Computing probe affinities (independent of data)... [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = verbose) - getProbeSequenceData.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #08. getProbeSequenceData(this, safe = safe, verbose = verbose) - getProbeSequenceData() is in environment
Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name
Hi, I've never seen that before, but remove any *.tmp or *.tmp.tmp etc files and try again. If that does not work, then please 1. show your script exactly at it is, 2. show the output you get from library(aroma.affymetrix); sessionInfo(); /Henrik. On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpat...@gmail.com wrote: Thanks Much Henrik. I used the ACS file, but I am not able to go further than the process(). I am getting an error Error: Failed to rename temporary file: probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp - probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp In addition: Warning messages: 1: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason 'Permission denied' 2: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36', reason 'Permission denied' 3: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf', reason 'Permission denied' 4: In file.remove(pathnameT) : cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d', reason 'Permission denied' Thanks, Rajesh. On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote: Hello All, I am getting the following error when doing process in aroma: csB - process(bc,verbose=TRUE); Background correcting data set... Computing probe affinities (independent of data)... [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = verbose) - getProbeSequenceData.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #08. getProbeSequenceData(this, safe = safe, verbose = verbose) - getProbeSequenceData() is in environment 'aroma.affymetrix' at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., verbose = less(verbose)) - computeAffinities.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #06. computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose)) - computeAffinities() is in environment 'aroma.affymetrix' at #05. bgAdjustGcrma.AffymetrixCelSet(structure(NA, .env = environment, class = c(AffymetrixCelSet, AffymetrixFileSet, AromaPlatformInterface, AromaMicroarrayDataSet, GenericDataFileSet, FullNameInterface, Object)), path = probeData/GSE4757,GRBC/HG-U133_Plus_2, verbose = structure(TRUE, .env = environment, class = c(Verbose, Object)), overwrite = FALSE, subsetToUpdate = NULL, typesToUpdate = pm, indicesNegativeControl = NULL, affinities = NULL, type = fullmodel, opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = NULL, .deprecated = FALSE) - bgAdjustGcrma.AffymetrixCelSet() is in environment 'aroma.affymetrix' at #04. bgAdjustGcrma(structure(NA, .env = environment, class = c(AffymetrixCelSet, AffymetrixFileSet, AromaPlatformInterface, AromaMicroarrayDataSet, GenericDataFileSet, FullNameInterface, Object)), path = probeData/GSE4757,GRBC/HG-U133_Plus_2, verbose = structure(TRUE, .env = environment, class = c(Verbose, Object)), overwrite = FALSE, subsetToUpdate = NULL, typesToUpdate = pm, indicesNegativeControl = NULL, affinities = NULL, type = fullmodel, opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = NULL, .deprecated = FALSE) - bgAdjustGcrma() is in environment 'aroma.affymetrix' at #03. do.call(bgAdjustGcrma, args = args) - do.call() is in environment 'base' at #02. process.GcRmaBackgroundCorrection(bc, verbose = TRUE) - process.GcRmaBackgroundCorrection() is in environment 'aroma.affymetrix' at #01. process(bc, verbose = TRUE) - process() is in environment 'aroma.core' Error: Computing probe affinities (independent of data)...done Background correcting data set...done Here is my directory structure : annotationData annotationData\chipTypes\HG-U133_Plus_2 11/03/2012 03:09 PMDIR . 11/03/2012 03:09 PMDIR .. 10/19/2012 10:49 AM99,044,850 HG-U133_Plus_2 - ascii.cdf 10/26/2012 09:49 PM26,251,783 HG-U133_Plus_2.cdf 10/29/2012 10:21 AM15,952,085 Hs133P_Hs_REFSEQ.cdf 07/14/2005 12:23 AM23,991,168 u133plus2gb_probe_tab rawData\GSE4757\HG-U133_Plus_2 10/26/2012 09:18 PMDIR . 10/26/2012 09:18 PMDIR .. 10/26/2012 09:17 PM13,555,389 GSM107522.cel 10/26/2012 09:17 PM13,556,785 GSM107523.cel 10/26/2012 09:17 PM13,560,384 GSM107524.cel 10/26/2012 09:17 PM13,556,716 GSM107525.cel 10/26/2012 09:17
