Messages by Date
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2011/10/31
[aroma.affymetrix] Problem with doCRMAv2 on Mapping250K_Nsp+Mapping250K_Sty chip
Ivan Smirnov
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2011/10/26
Re: [aroma.affymetrix] Digest for aroma-affymetrix@googlegroups.com - 2 Messages in 1 Topic
Henrik Bengtsson
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2011/10/26
Re: [aroma.affymetrix] Digest for aroma-affymetrix@googlegroups.com - 2 Messages in 1 Topic
Ivan Smirnov
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2011/10/25
Re: [aroma.affymetrix] Digest for aroma-affymetrix@googlegroups.com - 2 Messages in 1 Topic
Henrik Bengtsson
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2011/10/25
Re: [aroma.affymetrix] Digest for aroma-affymetrix@googlegroups.com - 2 Messages in 1 Topic
Ivan Smirnov
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2011/10/24
Re: [aroma.affymetrix] Problem with doCRMAv2
Pierre Neuvial
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2011/10/24
Re: [aroma.affymetrix] Problem with doCRMAv2
Ivan Smirnov
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2011/10/23
[aroma.affymetrix] Re: the time-cost of running aroma.affymetrix
marco
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2011/10/22
Re: [aroma.affymetrix] Re: the time-cost of running aroma.affymetrix
Henrik Bengtsson
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2011/10/21
[aroma.affymetrix] Re: the time-cost of running aroma.affymetrix
marco
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2011/10/21
Re: FW: [aroma.affymetrix] Naive Genotyping in Mouse
Henrik Bengtsson
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2011/10/21
Re: [aroma.affymetrix] the time-cost of running aroma.affymetrix
Henrik Bengtsson
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2011/10/21
[aroma.affymetrix] the time-cost of running aroma.affymetrix
marco
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2011/10/18
Re: [aroma.affymetrix] warnings and error message in reading affy snp6.0 cel file
Henrik Bengtsson
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2011/10/18
Re: [aroma.affymetrix] warnings and error message in reading affy snp6.0 cel file
Pierre Neuvial
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2011/10/18
[aroma.affymetrix] Regarding mergeGroups=FALSE / TRUE option in ExonRmaPlm()
rahul
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2011/10/18
[aroma.affymetrix] warnings and error message in reading affy snp6.0 cel file
Qian
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2011/10/18
[aroma.affymetrix] FIRMA on subset of normalized samples
rene.rotterdam
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2011/10/14
[aroma.affymetrix] FIRMA Scores in unit, group and cell columns for HuEx-1.0
rene.rotterdam
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2011/10/10
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/10/10
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
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2011/10/10
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/10/10
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
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2011/10/10
[aroma.affymetrix] Re: Processing HuEx-1_0-st-v2 exon array data
rahul
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2011/10/10
Re: [aroma.affymetrix] Processing HuEx-1_0-st-v2 exon array data
Henrik Bengtsson
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2011/10/10
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/10/10
[aroma.affymetrix] Processing HuEx-1_0-st-v2 exon array data
rahul
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2011/10/07
SV: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
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2011/10/06
Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Henrik Bengtsson
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2011/10/06
SV: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
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2011/10/06
Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Henrik Bengtsson
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2011/10/06
[aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
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2011/10/03
Re: [aroma.affymetrix] Naive Genotyping in Mouse
Henrik Bengtsson
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2011/10/03
[aroma.affymetrix] Naive Genotyping in Mouse
Rico.Daniel
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2011/09/30
Re: [aroma.affymetrix] Re: Human Exon Array ST Analysis
Henrik Bengtsson
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2011/09/30
[aroma.affymetrix] Re: Human Exon Array ST Analysis
rene.rotterdam
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2011/09/24
Re: [aroma.affymetrix] normalizing human ST arrays only using polya spike-ins
Henrik Bengtsson
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2011/09/24
Re: [aroma.affymetrix] Errors in mouse arrays (MOUSEDIVm520650)
Henrik Bengtsson
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2011/09/24
[aroma.affymetrix] Errors in mouse arrays (MOUSEDIVm520650)
Rico.Daniel
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2011/09/21
Re: [aroma.affymetrix] Human Exon Array ST Analysis
Henrik Bengtsson
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2011/09/21
Re: [aroma.affymetrix] signal detection
Henrik Bengtsson
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2011/09/21
RE: [aroma.affymetrix] computing firma scores on a subset of CEL files
Tarca, Adi
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2011/09/21
Re: [aroma.affymetrix] computing firma scores on a subset of CEL files
Henrik Bengtsson
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2011/09/21
[aroma.affymetrix] computing firma scores on a subset of CEL files
Tarca, Adi
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2011/09/17
[aroma.affymetrix] detection call
marco
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2011/09/17
[aroma.affymetrix] signal detection
marco
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2011/09/15
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/09/15
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
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2011/09/15
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/09/15
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
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2011/09/15
[aroma.affymetrix] Re: Error reading .cel files
rahul
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2011/09/15
Re: [aroma.affymetrix] Error reading .cel files
Henrik Bengtsson
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2011/09/15
[aroma.affymetrix] Error reading .cel files
rahul
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2011/09/13
[aroma.affymetrix] Human Exon Array ST Analysis
rene.rotterdam
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2011/09/07
[aroma.affymetrix] normalizing human ST arrays only using polya spike-ins
Richard Beyer
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2011/09/05
Re: [aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
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2011/09/05
Re: [aroma.affymetrix] Function Clash With IRanges
Henrik Bengtsson
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2011/09/04
Re: [aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
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2011/09/03
[aroma.affymetrix] aroma.affymetrix v2.2.0 released
Henrik Bengtsson
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2011/09/02
Re: [aroma.affymetrix] Function Clash With IRanges
Henrik Bengtsson
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2011/09/02
[aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
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2011/08/31
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
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2011/08/31
Re: Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
sean nj
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2011/08/31
Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
feugeas jean-paul
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2011/08/30
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
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2011/08/30
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
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2011/08/30
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
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2011/08/30
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
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2011/08/30
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
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2011/08/30
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
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2011/08/30
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
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2011/08/30
Re: Re : Re: [aroma.affymetrix] RAM scale factor
sean nj
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2011/08/30
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
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2011/08/29
Re: Re : Re: [aroma.affymetrix] RAM scale factor
Henrik Bengtsson
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2011/08/29
Re : Re: [aroma.affymetrix] RAM scale factor
feugeas jean-paul
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2011/08/27
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
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2011/08/27
Re: [aroma.affymetrix] MoGene ST 1.0 CDF file
Henrik Bengtsson
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2011/08/27
Re: [aroma.affymetrix] problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
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2011/08/27
Re: [aroma.affymetrix] RAM scale factor
Henrik Bengtsson
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2011/08/26
[aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Irina Ostrovnaya
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2011/08/25
[aroma.affymetrix] MoGene ST 1.0 CDF file
sabrina
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2011/08/24
[aroma.affymetrix] problem processing output of AllelicCrosstalkCalibration
DGoode
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2011/08/22
Re: [aroma.affymetrix] Normalizing Hs_PromPR_v02 data
aik seng Ooi
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2011/08/22
[aroma.affymetrix] Normalizing Hs_PromPR_v02 data
Aikseng
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2011/08/17
[aroma.affymetrix] RAM scale factor
feugeas jean-paul
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2011/08/12
[aroma.affymetrix] Re: Cannot read .cel files for chip type HuEx-1_0-st-v2
Matthew Weiser
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2011/08/11
Re: [aroma.affymetrix] Cannot read .cel files for chip type HuEx-1_0-st-v2
Henrik Bengtsson
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2011/08/10
[aroma.affymetrix] Cannot read .cel files for chip type HuEx-1_0-st-v2
Matthew Weiser
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2011/08/09
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Mark Robinson
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2011/08/09
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
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2011/08/09
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Mark Robinson
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2011/08/09
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Pierre Neuvial
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2011/08/08
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
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2011/08/08
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
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2011/08/08
Re: [aroma.affymetrix] How to extract raw probe intensity from .CEL file
Pierre Neuvial
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2011/08/08
[aroma.affymetrix] How to extract raw probe intensity from .CEL file
hsingjun cheung
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2011/08/05
Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file
Yaping Feng
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2011/08/05
Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file
Pierre Neuvial
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2011/08/05
[aroma.affymetrix] aroma.affymetrix can't read cdf file
Yaping Feng
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2011/07/14
Re: Downstream gene expression analysis? (Was: Re: [aroma.affymetrix] Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files)
Henrik Bengtsson
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2011/07/14
Re: Downstream gene expression analysis? (Was: Re: [aroma.affymetrix] Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files)
sean nj
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2011/07/14
[aroma.affymetrix] Re: Problem creating csU MAT normalization
Jill
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2011/07/13
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
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2011/07/13
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Kasper Daniel Hansen
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2011/07/13
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
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2011/07/13
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
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2011/07/13
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
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2011/07/13
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
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2011/07/13
Re: [aroma.affymetrix] convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
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2011/07/13
[aroma.affymetrix] convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
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2011/07/12
[aroma.affymetrix] Re: Accessing individual probe intensities
Maria Rodrigo-Domingo
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2011/07/11
Re: [aroma.affymetrix] Re: Problem creating csU MAT normalization
Henrik Bengtsson
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2011/07/11
Re: [aroma.affymetrix] Re: Accessing individual probe intensities
Henrik Bengtsson
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2011/07/11
Re: [aroma.affymetrix] exon level data.frame dimensions
Henrik Bengtsson
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2011/07/11
[aroma.affymetrix] exon level data.frame dimensions
Anita
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2011/07/11
[aroma.affymetrix] Re: FIRMA: using setMergeGroups() for ExonRmaPlm to define groups
Marlen Mueller
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2011/07/10
[aroma.affymetrix] Re: Accessing individual probe intensities
Maria Rodrigo-Domingo
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2011/07/10
[aroma.affymetrix] Re: Problem creating csU MAT normalization
Jill
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2011/07/10
[aroma.affymetrix] Problem creating csU MAT normalization
Jill
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2011/07/09
Re: Downstream gene expression analysis? (Was: Re: [aroma.affymetrix] Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files)
Henrik Bengtsson
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2011/07/09
Re: [aroma.affymetrix] Re: Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
Henrik Bengtsson
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2011/07/09
Re: [aroma.affymetrix] Accessing individual probe intensities
Henrik Bengtsson
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2011/07/08
[aroma.affymetrix] Re: Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
sean nj
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2011/07/08
[aroma.affymetrix] Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
sean nj
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2011/07/08
[aroma.affymetrix] Problem with custome CDF for affy HG-U133_Plus_2 data analysis.
sean nj
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2011/07/08
[aroma.affymetrix] Problem with custome CDF for affy HG-U133_Plus_2 data analysis.
sean nj
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2011/07/06
[aroma.affymetrix] Accessing individual probe intensities
Maria Rodrigo-Domingo
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2011/07/04
[aroma.affymetrix] FIRMA: using setMergeGroups() for ExonRmaPlm to define groups
marlibu
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2011/06/28
Re: [aroma.affymetrix] Error in list(`process(acc)` = <environment>, `process.AllelicCrosstalkCalibration(acc)` = <environment>, Exception: Failed to retrieve genome information for this chip type:
sean nj
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2011/06/27
Re: [aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Henrik Bengtsson
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2011/06/27
Re: [aroma.affymetrix] append() for celSets
Henrik Bengtsson
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2011/06/27
Re: [aroma.affymetrix] Error in list(`process(acc)` = <environment>, `process.AllelicCrosstalkCalibration(acc)` = <environment>, Exception: Failed to retrieve genome information for this chip type:
Henrik Bengtsson
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2011/06/27
[aroma.affymetrix] Error in list(`process(acc)` = <environment>, `process.AllelicCrosstalkCalibration(acc)` = <environment>, Exception: Failed to retrieve genome information for this chip type:
sean nj
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2011/06/26
[aroma.affymetrix] append() for celSets
Dario Strbenac
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2011/06/26
[aroma.affymetrix] Re: Question about Firma
Mark Robinson
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2011/06/22
Re: [aroma.affymetrix] Re: gcRMA for Gene ST Arrays
Mark Robinson
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2011/06/21
[aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Kai
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2011/06/17
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Xavi Sole
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2011/06/17
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Henrik Bengtsson
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2011/06/17
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Henrik Bengtsson
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2011/06/17
Re: [aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Henrik Bengtsson
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2011/06/17
Re: [aroma.affymetrix] Processing multiple Affymetrix arrays
Henrik Bengtsson
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2011/06/17
[aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Kai
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2011/06/16
[aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Xavi Sole
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2011/06/08
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
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2011/06/07
Re: [aroma.affymetrix] Error in rescale(..) during allelic crosstalk calibration
Henrik Bengtsson
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2011/06/07
[aroma.affymetrix] Error in rescale(..) during allelic crosstalk calibration
David JH Shih
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2011/06/07
[aroma.affymetrix] log ratios of copy number
Yan Jiao
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2011/06/07
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Henrik Bengtsson
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2011/06/01
[aroma.affymetrix] Details on the CalMaTe method
Jonas
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2011/05/31
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
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2011/05/31
RE: [aroma.affymetrix] copy number gain /loss
Yan Jiao
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2011/05/30
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
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2011/05/30
[aroma.affymetrix] Re: GWS_6 hg19
cstratowa
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2011/05/27
Re: [aroma.affymetrix] Re: GWS_6 hg19
Henrik Bengtsson
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2011/05/27
Re: [aroma.affymetrix] Affy 6.0 paired copy number analysis
Henrik Bengtsson
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2011/05/27
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Henrik Bengtsson
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2011/05/27
[aroma.affymetrix] Affy 6.0 paired copy number analysis
Xavi Solé
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2011/05/27
[aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
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2011/05/27
[aroma.affymetrix] Re: GWS_6 hg19
cstratowa
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2011/05/26
Re: [aroma.affymetrix] Re: GWS_6 hg19
Henrik Bengtsson
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2011/05/26
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
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2011/05/26
RE: [aroma.affymetrix] copy number gain /loss
Yan Jiao
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2011/05/26
[aroma.affymetrix] Re: GWS_6 hg19
cstratowa
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2011/05/25
Re: [aroma.affymetrix] Re: GWS_6 hg19
Henrik Bengtsson
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2011/05/25
Re: [aroma.affymetrix] Combine paired and unpaired CN analysis
Henrik Bengtsson
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2011/05/25
Re: [aroma.affymetrix] CBS using doCRMAv2 and CalMaTe
Henrik Bengtsson
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2011/05/25
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
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2011/05/25
[aroma.affymetrix] copy number gain /loss
Yan Jiao
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2011/05/23
[aroma.affymetrix] Combine paired and unpaired CN analysis
Kai
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2011/05/21
Re: [aroma.affymetrix] Re: Probe genomic location
Henrik Bengtsson
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2011/05/20
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/20
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/18
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/18
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/18
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/18
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
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2011/05/17
Re: [aroma.affymetrix] Probe genomic location
Henrik Bengtsson
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2011/05/17
[aroma.affymetrix] Probe genomic location
Irene Pylypenko
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2011/05/16
[aroma.affymetrix] Re: CustomCDF usage error
Fong
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2011/05/16
Re: [aroma.affymetrix] Re: CustomCDF usage error
Henrik Bengtsson
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2011/05/16
[aroma.affymetrix] Re: CustomCDF usage error
Fong
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2011/05/16
[aroma.affymetrix] CBS using doCRMAv2 and CalMaTe
mortiz
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2011/05/15
Re: [aroma.affymetrix] CustomCDF usage error
Henrik Bengtsson
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2011/05/15
Re: [aroma.affymetrix] sfit fails
Henrik Bengtsson
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2011/05/12
[aroma.affymetrix] sfit fails
jasmine
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2011/05/10
[aroma.affymetrix] Re: FIRMA problem, master thesis
Elizabeth Purdom
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2011/05/05
Re: [aroma.affymetrix] Re: AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
Henrik Bengtsson
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2011/05/05
[aroma.affymetrix] Re: AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
richland
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2011/05/05
Re: [aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
Henrik Bengtsson
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2011/05/05
[aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
richland
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2011/05/04
[aroma.affymetrix] CustomCDF usage error
Fong
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2011/05/02
[aroma.affymetrix] GenomeGraphs FIRMA scores heatmap question
dbe...@u.washington.edu
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2011/04/28
[aroma.affymetrix] Firma on CustomCDF
Fong
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2011/04/25
Re: [aroma.affymetrix] CRLMM support for Affy 6.0 chips?
Henrik Bengtsson
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2011/04/22
[aroma.affymetrix] CRLMM support for Affy 6.0 chips?
HWright
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2011/04/20
[aroma.affymetrix] exon and psr
sabrina
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2011/04/15
Re: getAverageFile() or calculateBaseline() for the CN reference? (Was: Re: [aroma.affymetrix] AromaUnitTotalCnBinarySet vs CnChipEffectSet)
Henrik Bengtsson
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2011/04/15
Re: [aroma.affymetrix] AromaUnitTotalCnBinarySet vs CnChipEffectSet
Henrik Bengtsson
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2011/04/15
Re: Probe-level summarization with "unique" CDFs? (Was: Re: [aroma.affymetrix] aroma.affymetrix v2.1.0 released)
Henrik Bengtsson