*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 *
* *
--
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