aroma-affymetrix
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[aroma.affymetrix] Processing HuEx-1_0-st-v2 exon array data
rahul
Re: [aroma.affymetrix] Processing HuEx-1_0-st-v2 exon array data
Henrik Bengtsson
[aroma.affymetrix] Re: Processing HuEx-1_0-st-v2 exon array data
rahul
[aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Henrik Bengtsson
SV: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Henrik Bengtsson
SV: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using AffymetrixCelSet$byName
Johan Staaf
[aroma.affymetrix] Naive Genotyping in Mouse
Rico.Daniel
Re: [aroma.affymetrix] Naive Genotyping in Mouse
Henrik Bengtsson
Re: FW: [aroma.affymetrix] Naive Genotyping in Mouse
Henrik Bengtsson
[aroma.affymetrix] Re: Naive Genotyping in Mouse
Irsan Kooi
[aroma.affymetrix] Errors in mouse arrays (MOUSEDIVm520650)
Rico.Daniel
Re: [aroma.affymetrix] Errors in mouse arrays (MOUSEDIVm520650)
Henrik Bengtsson
[aroma.affymetrix] detection call
marco
[aroma.affymetrix] signal detection
marco
Re: [aroma.affymetrix] signal detection
Henrik Bengtsson
[aroma.affymetrix] Error reading .cel files
rahul
Re: [aroma.affymetrix] Error reading .cel files
Henrik Bengtsson
[aroma.affymetrix] Re: Error reading .cel files
rahul
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
[aroma.affymetrix] Re: Error reading .cel files
rahul
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
[aroma.affymetrix] Re: Error reading .cel files
rahul
[aroma.affymetrix] Re: Error reading .cel files
rahul
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
[aroma.affymetrix] Re: Error reading .cel files
rahul
Re: [aroma.affymetrix] Re: Error reading .cel files
Henrik Bengtsson
[aroma.affymetrix] Re: Error reading .cel files
rahul
[aroma.affymetrix] Human Exon Array ST Analysis
rene.rotterdam
Re: [aroma.affymetrix] Human Exon Array ST Analysis
Henrik Bengtsson
[aroma.affymetrix] Re: Human Exon Array ST Analysis
rene.rotterdam
Re: [aroma.affymetrix] Re: Human Exon Array ST Analysis
Henrik Bengtsson
[aroma.affymetrix] normalizing human ST arrays only using polya spike-ins
Richard Beyer
Re: [aroma.affymetrix] normalizing human ST arrays only using polya spike-ins
Henrik Bengtsson
[aroma.affymetrix] aroma.affymetrix v2.2.0 released
Henrik Bengtsson
[aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
Re: [aroma.affymetrix] Function Clash With IRanges
Henrik Bengtsson
Re: [aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
Re: [aroma.affymetrix] Function Clash With IRanges
Henrik Bengtsson
Re: [aroma.affymetrix] Function Clash With IRanges
Dario Strbenac
[aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Irina Ostrovnaya
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
Re: [aroma.affymetrix] errors in AffymetrixCelSet$byName and process(acc, verbose=verbose)
Henrik Bengtsson
[aroma.affymetrix] MoGene ST 1.0 CDF file
sabrina
Re: [aroma.affymetrix] MoGene ST 1.0 CDF file
Henrik Bengtsson
[aroma.affymetrix] problem processing output of AllelicCrosstalkCalibration
DGoode
Re: [aroma.affymetrix] problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Henrik Bengtsson
[aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
DGoode
[aroma.affymetrix] Normalizing Hs_PromPR_v02 data
Aikseng
Re: [aroma.affymetrix] Normalizing Hs_PromPR_v02 data
aik seng Ooi
[aroma.affymetrix] RAM scale factor
feugeas jean-paul
Re: [aroma.affymetrix] RAM scale factor
Henrik Bengtsson
Re : Re: [aroma.affymetrix] RAM scale factor
feugeas jean-paul
Re: Re : Re: [aroma.affymetrix] RAM scale factor
Henrik Bengtsson
Re: Re : Re: [aroma.affymetrix] RAM scale factor
sean nj
Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
feugeas jean-paul
Re: Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
sean nj
[aroma.affymetrix] Cannot read .cel files for chip type HuEx-1_0-st-v2
Matthew Weiser
Re: [aroma.affymetrix] Cannot read .cel files for chip type HuEx-1_0-st-v2
Henrik Bengtsson
[aroma.affymetrix] Re: Cannot read .cel files for chip type HuEx-1_0-st-v2
Matthew Weiser
[aroma.affymetrix] How to extract raw probe intensity from .CEL file
hsingjun cheung
Re: [aroma.affymetrix] How to extract raw probe intensity from .CEL file
Pierre Neuvial
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Pierre Neuvial
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Mark Robinson
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Mark Robinson
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
hsingjun cheung
[aroma.affymetrix] aroma.affymetrix can't read cdf file
Yaping Feng
Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file
Pierre Neuvial
Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file
Yaping Feng
[aroma.affymetrix] convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
Re: [aroma.affymetrix] convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Henrik Bengtsson
Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
Kasper Daniel Hansen
[aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM
sean nj
[aroma.affymetrix] exon level data.frame dimensions
Anita
Re: [aroma.affymetrix] exon level data.frame dimensions
Henrik Bengtsson
[aroma.affymetrix] Problem creating csU MAT normalization
Jill
[aroma.affymetrix] Re: Problem creating csU MAT normalization
Jill
Re: [aroma.affymetrix] Re: Problem creating csU MAT normalization
Henrik Bengtsson
[aroma.affymetrix] Re: Problem creating csU MAT normalization
Jill
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
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
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
[aroma.affymetrix] Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
sean nj
[aroma.affymetrix] Re: Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
sean nj
Re: [aroma.affymetrix] Re: Problems with custom CDF when doing RMA on affy HG-U133_Plus_2 chip CEL files
Henrik Bengtsson
[aroma.affymetrix] Problem with custome CDF for affy HG-U133_Plus_2 data analysis.
sean nj
[aroma.affymetrix] Problem with custome CDF for affy HG-U133_Plus_2 data analysis.
sean nj
[aroma.affymetrix] Accessing individual probe intensities
Maria Rodrigo-Domingo
Re: [aroma.affymetrix] Accessing individual probe intensities
Henrik Bengtsson
[aroma.affymetrix] Re: Accessing individual probe intensities
Maria Rodrigo-Domingo
Re: [aroma.affymetrix] Re: Accessing individual probe intensities
Henrik Bengtsson
[aroma.affymetrix] Re: Accessing individual probe intensities
Maria Rodrigo-Domingo
[aroma.affymetrix] FIRMA: using setMergeGroups() for ExonRmaPlm to define groups
marlibu
[aroma.affymetrix] Re: FIRMA: using setMergeGroups() for ExonRmaPlm to define groups
Marlen Mueller
[aroma.affymetrix] Error in list(`process(acc)` = <environment>, `process.AllelicCrosstalkCalibration(acc)` = <environment>, Exception: Failed to retrieve genome information for this chip type:
sean nj
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
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
[aroma.affymetrix] computing firma scores on a subset of CEL files
Tarca, Adi
Re: [aroma.affymetrix] computing firma scores on a subset of CEL files
Henrik Bengtsson
RE: [aroma.affymetrix] computing firma scores on a subset of CEL files
Tarca, Adi
[aroma.affymetrix] append() for celSets
Dario Strbenac
Re: [aroma.affymetrix] append() for celSets
Henrik Bengtsson
[aroma.affymetrix] Re: Question about Firma
Mark Robinson
Re: [aroma.affymetrix] Re: gcRMA for Gene ST Arrays
Mark Robinson
Re: [aroma.affymetrix] Re: gcRMA for Gene ST Arrays
dbe...@u.washington.edu
[aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Xavi Sole
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Henrik Bengtsson
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Henrik Bengtsson
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Xavi Sole
[aroma.affymetrix] Error in rescale(..) during allelic crosstalk calibration
David JH Shih
Re: [aroma.affymetrix] Error in rescale(..) during allelic crosstalk calibration
Henrik Bengtsson
[aroma.affymetrix] Details on the CalMaTe method
Jonas
[aroma.affymetrix] Affy 6.0 paired copy number analysis
Xavi Solé
Re: [aroma.affymetrix] Affy 6.0 paired copy number analysis
Henrik Bengtsson
[aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Henrik Bengtsson
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Henrik Bengtsson
[aroma.affymetrix] log ratios of copy number
Yan Jiao
Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0
Ravi Sharma
[aroma.affymetrix] copy number gain /loss
Yan Jiao
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
RE: [aroma.affymetrix] copy number gain /loss
Yan Jiao
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
RE: [aroma.affymetrix] copy number gain /loss
Yan Jiao
Re: [aroma.affymetrix] copy number gain /loss
Henrik Bengtsson
[aroma.affymetrix] Combine paired and unpaired CN analysis
Kai
Re: [aroma.affymetrix] Combine paired and unpaired CN analysis
Henrik Bengtsson
[aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Kai
Re: [aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Henrik Bengtsson
[aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Kai
Re: [aroma.affymetrix] Re: Combine paired and unpaired CN analysis
Henrik Bengtsson
[aroma.affymetrix] Probe genomic location
Irene Pylypenko
Re: [aroma.affymetrix] Probe genomic location
Henrik Bengtsson
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
[aroma.affymetrix] Re: Probe genomic location
Irene Pylypenko
Re: [aroma.affymetrix] Re: Probe genomic location
Henrik Bengtsson
[aroma.affymetrix] CBS using doCRMAv2 and CalMaTe
mortiz
Re: [aroma.affymetrix] CBS using doCRMAv2 and CalMaTe
Henrik Bengtsson
[aroma.affymetrix] sfit fails
jasmine
Re: [aroma.affymetrix] sfit fails
Henrik Bengtsson
[aroma.affymetrix] Re: FIRMA problem, master thesis
Elizabeth Purdom
[aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
richland
Re: [aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
Henrik Bengtsson
[aroma.affymetrix] Re: AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
richland
Re: [aroma.affymetrix] Re: AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0
Henrik Bengtsson
[aroma.affymetrix] CustomCDF usage error
Fong
Re: [aroma.affymetrix] CustomCDF usage error
Henrik Bengtsson
[aroma.affymetrix] Re: CustomCDF usage error
Fong
Re: [aroma.affymetrix] Re: CustomCDF usage error
Henrik Bengtsson
[aroma.affymetrix] Re: CustomCDF usage error
Fong
[aroma.affymetrix] GenomeGraphs FIRMA scores heatmap question
dbe...@u.washington.edu
[aroma.affymetrix] Firma on CustomCDF
Fong
[aroma.affymetrix] CRLMM support for Affy 6.0 chips?
HWright
Re: [aroma.affymetrix] CRLMM support for Affy 6.0 chips?
Henrik Bengtsson
[aroma.affymetrix] exon and psr
sabrina
Re: getAverageFile() or calculateBaseline() for the CN reference? (Was: Re: [aroma.affymetrix] AromaUnitTotalCnBinarySet vs CnChipEffectSet)
Henrik Bengtsson
Re: Probe-level summarization with "unique" CDFs? (Was: Re: [aroma.affymetrix] aroma.affymetrix v2.1.0 released)
Henrik Bengtsson
[aroma.affymetrix] Combining paired and unpaired analysis
Kai
[aroma.affymetrix] For detecting alternate splicing, which algorithm should I use?
James
[aroma.affymetrix] AromaUnitTotalCnBinarySet vs CnChipEffectSet
Kai
Re: [aroma.affymetrix] AromaUnitTotalCnBinarySet vs CnChipEffectSet
Henrik Bengtsson
[aroma.affymetrix] aroma.affymetrix v2.1.0 released
Henrik Bengtsson
RE: [aroma.affymetrix] aroma.affymetrix v2.1.0 released
Hooiveld, Guido
[aroma.affymetrix] gcRMA-HuEx-1_0-st-v2 problem
James
Re: [aroma.affymetrix] gcRMA-HuEx-1_0-st-v2 problem
Henrik Bengtsson
[aroma.affymetrix] Re: gcRMA-HuEx-1_0-st-v2 problem
James
Re: [aroma.affymetrix] Re: gcRMA-HuEx-1_0-st-v2 problem
Henrik Bengtsson
[aroma.affymetrix] Re: gcRMA-HuEx-1_0-st-v2 problem
James
[aroma.affymetrix] question about how to get the gene centric values for a probe set?
xiaowei guan
Re: [aroma.affymetrix] question about how to get the gene centric values for a probe set?
Henrik Bengtsson
[aroma.affymetrix] Importing plier expression from APT
Fong
Re: [aroma.affymetrix] Importing plier expression from APT
Henrik Bengtsson
[aroma.affymetrix] Bioinformatics Opening @ Barts Cancer Institute
Claude Chelala
Re: Filtering out loci downstream of CRMAv2 (Was: Re: [aroma.affymetrix] Re: AromaUnitTotalCnBinarySet Manipulation)
Henrik Bengtsson
[aroma.affymetrix] output of Affy Nsp and Sty calls in .ped / .map format
Herbeck
Re: [aroma.affymetrix] output of Affy Nsp and Sty calls in .ped / .map format
Henrik Bengtsson
[aroma.affymetrix] RasterImage problem upon installation/update aroma.affymetrix
AC
Re: [aroma.affymetrix] RasterImage problem upon installation/update aroma.affymetrix
Henrik Bengtsson
[aroma.affymetrix] Re: RasterImage problem upon installation/update aroma.affymetrix
AC
Re: [aroma.affymetrix] Re: RasterImage problem upon installation/update aroma.affymetrix
Henrik Bengtsson
[aroma.affymetrix] Aroma Affymetrix shell variable path?
Fong
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