On Thu, Nov 22, 2012 at 6:35 AM, Raj Patrao <[email protected]> wrote:
> Hello Henrik, thanks for the reply.
>
> the tmp folder is within the GSE4757,GRBC folder, which is not getting
> renamed (throwing error).
Which tmp folder, what's the error message and in what step is this created?
/Henrik
>
> -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
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> traceback(), and 3) to post a complete code example.
>
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--
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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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