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-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
