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_0.8.2 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 <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 '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
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to aroma-af...@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.
>
>
> 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.
You received this message because you are subscribed to the Google Groups
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