Respected Dr Bengtsson,
I have the following codes and outputs:
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
Filesize: 203.31MB
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 297051
Cells per unit: 22.06
Number of QC units: 1
> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
> print(ptf)
AffymetrixProbeTabFile:
Name: HuEx-1_0-st-v2
Tags:
Full name: HuEx-1_0-st-v2
Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
File size: 527.80 MB (553438704 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly',
'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness',
'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/HuEx-1_0-st-v2
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Number of arrays: 17
Names: 10_5N, 11_6T, ..., 9_5T
Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
Total file size: 1081.22MB
RAM: 0.02MB
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
> print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 17 (1081.22MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
20101202 14:46:02|Background correcting data set...
20101202 14:46:02| Computing probe affinities (independent of data)...
20101202 14:46:03| Computing GCRMA probe affinities...
20101202 14:46:03| Chip type: HuEx-1_0-st-v2
20101202 14:46:03| Number of units: 297051
20101202 14:46:03| Locating the cell sequence annotation data file...
20101202 14:46:03| Locating the cell sequence annotation data file...done
20101202 14:46:03| Computing GCRMA probe affinities...done
20101202 14:46:03| Computing GCRMA probe affinities...
20101202 14:46:03| Number of units: 297051
20101202 14:46:03| Identify PMs and MMs among the CDF cell indices...
logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode TRUE NA's
logical 5270074 0
20101202 14:46:52| MMs are defined as non-PMs
20101202 14:46:52| Number of PMs: 5270074
20101202 14:46:52| Number of MMs: 0
20101202 14:46:52| Identify PMs and MMs among the CDF cell indices...done
20101202 14:46:52| Reading probe-sequence data...
20101202 14:46:52| Retrieving probe-sequence data...
20101202 14:46:52| Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
20101202 14:46:52| Locating probe-tab file...
20101202 14:46:52| Chip type: HuEx-1_0-st-v2
AffymetrixProbeTabFile:
Name: HuEx-1_0-st-v2
Tags:
Full name: HuEx-1_0-st-v2
Pathname:
annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
File size: 527.80 MB (553438704 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
20101202 14:46:52| Locating probe-tab file...done
20101202 14:46:52| Validating probe-tab file against CDF...
20101202 14:46:52| Number of records read: 1
20101202 14:46:52| Data read:
'data.frame': 1 obs. of 1 variable:
$ probeSetID: chr "2315101"
- attr(*, "fileHeader")=List of 6
..$ comments: NULL
..$ sep : chr "\t"
..$ quote : chr "\""
..$ skip : num 0
..$ topRows :List of 10
.. ..$ : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ...
.. ..$ : chr "494998" "2315101" "917" "193" ...
.. ..$ : chr "1734213" "2315101" "1092" "677" ...
.. ..$ : chr "4767517" "2315101" "796" "1862" ...
.. ..$ : chr "4286427" "2315101" "986" "1674" ...
.. ..$ : chr "5760145" "2315102" "144" "2250" ...
.. ..$ : chr "671410" "2315102" "689" "262" ...
.. ..$ : chr "4275780" "2315102" "579" "1670" ...
.. ..$ : chr "4293462" "2315102" "341" "1677" ...
.. ..$ : chr "5388" "2315103" "267" "2" ...
..$ columns : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ...
20101202 14:46:52| Unit name:
chr "2315101"
20101202 14:46:55| Unit index: NA
Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
<environment>, :
[2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name
'2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
at throw(Exception(...))
at throw.default("Failed to identify CDF unit with unit name '", unitNa
at throw("Failed to identify CDF unit with unit name '", unitName, "':
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/HuEx-1_0-st-v2",
at do.call("bgAdjustGcrma", args = args)
at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
20101202 14:46:55| Validating probe-tab file against CDF...done
20101202 14:46:55| Retrieving probe-sequence data...done
20101202 14:46:55| Reading probe-sequence data...done
20101202 14:46:55| Computing GCRMA probe affinities...done
20101202 14:46:55| Computing probe affinities (independent of data)...done
20101202 14:46:55|Background correcting data set...done
Could you please tell me how to rectify the error?
Thank you.
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
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