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_0.8.2 R.cache_0.6.3
[10] R.devices_2.1.1 R.filesets_1.1.5 digest_0.5.2
[13] R.utils_1.18.0 R.oo_1.10.1 R.methodsS3_1.4.2
[16] e1071_1.6-1 class_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 <[email protected]<javascript:>>
> 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 PM <DIR> .
> >> 11/03/2012 03:09 PM <DIR> ..
> >> 10/19/2012 10:49 AM 99,044,850 HG-U133_Plus_2 - ascii.cdf
> >> 10/26/2012 09:49 PM 26,251,783 HG-U133_Plus_2.cdf
> >> 10/29/2012 10:21 AM 15,952,085 Hs133P_Hs_REFSEQ.cdf
> >> 07/14/2005 12:23 AM 23,991,168 u133plus2gb_probe_tab
> >>
> >> --------> rawData\GSE4757\HG-U133_Plus_2
> >>
> >> 10/26/2012 09:18 PM <DIR> .
> >> 10/26/2012 09:18 PM <DIR> ..
> >> 10/26/2012 09:17 PM 13,555,389 GSM107522.cel
> >> 10/26/2012 09:17 PM 13,556,785 GSM107523.cel
> >> 10/26/2012 09:17 PM 13,560,384 GSM107524.cel
> >> 10/26/2012 09:17 PM 13,556,716 GSM107525.cel
> >> 10/26/2012 09:17 PM 13,552,046 GSM107526.cel
> >> 10/26/2012 09:17 PM 13,552,689 GSM107527.cel
> >> 10/26/2012 09:17 PM 13,553,222 GSM107528.cel
> >> 10/26/2012 09:17 PM 13,552,445 GSM107529.cel
> >> 10/26/2012 09:17 PM 13,551,059 GSM107530.cel
> >> 10/26/2012 09:17 PM 13,550,482 GSM107531.cel
> >> 10/26/2012 09:17 PM 13,550,367 GSM107532.cel
> >> 10/26/2012 09:17 PM 13,550,546 GSM107533.cel
> >> 10/26/2012 09:17 PM 13,551,111 GSM107534.cel
> >> 10/26/2012 09:17 PM 13,551,023 GSM107535.cel
> >> 10/26/2012 09:17 PM 13,551,624 GSM107536.cel
> >> 10/26/2012 09:17 PM 13,550,386 GSM107537.cel
> >> 10/26/2012 09:17 PM 13,552,402 GSM107538.cel
> >> 10/26/2012 09:17 PM 13,552,977 GSM107539.cel
> >> 10/26/2012 09:18 PM 13,553,854 GSM107540.cel
> >> 10/26/2012 09:18 PM 13,553,795 GSM107541.cel
> >>
> >> I took the probe tab file from
> >> http://masker.nci.nih.gov/ev/U133Plus2gb_probe_tab.gz
> >>
> >> Please let me know what is wrong and how to proceed.
> >>
> >> Thanks,
> >> Raj
> >>
> >>
> >>
> >>
> > --
> > 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
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> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
> > To post to this group, send email to
> > [email protected]<javascript:>
> > To unsubscribe and other options, go to
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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.
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