Showing : Affy • reset
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Normalization of exon arrays with expected global RNA degradation
Normalization affy Normalization affy
14.2 years ago ekspiulo ▴ 40
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Some problems in combining ExpressionSet objects with the combine() function
Microarray GO Cancer Colon affy limma Microarray GO Cancer Colon affy limma
14.2 years ago James W. MacDonald 68k
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Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
updated 14.3 years ago by ▴ 590 • written 14.3 years ago by ★ 2.3k
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gcrma
affy gcrma affy gcrma
updated 14.3 years ago by ▴ 50 • written 14.3 years ago by ▴ 30
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1.1k
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altcdfenvs: mapping probes and creating new probe sets: guidance requested
cdf probe affy altcdfenvs cdf probe affy altcdfenvs
updated 14.3 years ago by 68k • written 14.3 years ago by ▴ 80
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Resend: altcdfenvs: mapping probes and creating new probe sets: guidance requested
cdf probe affy altcdfenvs cdf probe affy altcdfenvs
14.3 years ago Ariel Grostern ▴ 80
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2
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1.0k
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biobase
Biobase affy Biobase affy
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 10
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2
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1.3k
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AnnotationDbi:makeProbePackage for PM-only chips....getting closer.....now error in installation of probe package
cdf probe affy AnnotationDbi cdf probe affy AnnotationDbi
updated 14.3 years ago by 68k • written 14.3 years ago by ▴ 80
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2
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1.6k
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Affymetrix Gene Chip Normalization
Normalization affy oligo xps Normalization affy oligo xps
updated 14.3 years ago by ★ 3.9k • written 14.3 years ago by ▴ 30
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1.3k
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Converting makeProbePackage in AnnotationDbi to permit PM-only arrays
cdf probe affy altcdfenvs cdf probe affy altcdfenvs
14.3 years ago Ariel Grostern ▴ 80
0
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0
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797
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Follow-up: AnnotationDbi and makeProbePackage for PM-only Affy chips
Microarray affy AnnotationDbi Microarray affy AnnotationDbi
14.3 years ago Ariel Grostern ▴ 80
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7
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2.1k
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Working with Agilent 4X44k array,two color experiment
GO affy GO affy
updated 14.3 years ago by ▴ 70 • written 14.3 years ago by ▴ 200
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1.3k
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Re-annotation of probes for an Affy custom microarray
Annotation cdf affy Annotation cdf affy
updated 14.3 years ago by ★ 2.3k • written 14.3 years ago by ▴ 80
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cause 'memory not mapped'
Microarray Genetics Normalization affy Microarray Genetics Normalization affy
updated 14.3 years ago by ★ 1.3k • written 14.3 years ago by ▴ 10
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1.4k
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miRNA microarray analysis
miRNA affy siggenes miRNA affy siggenes
14.4 years ago Assa Yeroslaviz ★ 1.5k
0
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7
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1.9k
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vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 14.4 years ago by 68k • written 14.4 years ago by ▴ 370
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1
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1.3k
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RMA (affy) followed by SAM (samr)
rae230a rae230b cdf affy PROcess rae230a rae230b cdf affy PROcess
updated 14.4 years ago by ▴ 900 • written 14.4 years ago by ▴ 30
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1
reply
862
views
Eliminating Absent Data
probe affy probe affy
updated 14.4 years ago by 68k • written 14.4 years ago by ▴ 40
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1
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1.4k
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understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 14.4 years ago by 68k • written 14.4 years ago by ★ 1.5k
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4
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1.5k
views
Empty featureData in ExpressionSet generated by affy::justRMA
Annotation hgu133a2 probe affy Annotation hgu133a2 probe affy
updated 14.4 years ago by 68k • written 14.4 years ago by ▴ 30
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1
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1.1k
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Human Exon array annotation problem.
Annotation affy xmapcore Annotation affy xmapcore
updated 14.4 years ago by ▴ 190 • written 14.4 years ago by ▴ 970
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1.0k
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gcrma on affy xlaevis arrays
GO affy gcrma GO affy gcrma
14.4 years ago Tobias Straub ▴ 10
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1
reply
1.3k
views
Affymetrix 250K SNP aCGH
aCGH SNP Normalization affy aCGH aCGH SNP Normalization affy aCGH
updated 14.5 years ago by ▴ 210 • written 14.5 years ago by ▴ 330
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1.3k
views
Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
14.5 years ago Harris A. Jaffee ▴ 590
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1
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1.1k
views
customCDF name not recognized and switched to Affy CDF
cdf affy gcrma cdf affy gcrma
updated 14.5 years ago by 68k • written 14.5 years ago by ▴ 80
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1.1k
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Using DESeq or EdgeR for Exon Differential Expression Analysis
affy edgeR DESeq affy edgeR DESeq
14.5 years ago Davis McCarthy ▴ 260
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2
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1.8k
views
GoStats
Organism affy Organism affy
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 860
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2
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1.2k
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importing ID table in AnnotationDbi
Annotation affy Annotation affy
14.6 years ago Dana.Stanley@csiro.au ▴ 110
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1.2k
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Affy normalization and filtering method
Normalization Leukemia Lung hu6800 affy Normalization Leukemia Lung hu6800 affy
14.6 years ago Juliet Hannah ▴ 360
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1.4k
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quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
14.6 years ago Assa Yeroslaviz ★ 1.5k
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1
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1.0k
views
affymetrix miRNA QC Tool vs expresso data discrepancy
cdf affy cdf affy
updated 14.6 years ago by 68k • written 14.6 years ago by ▴ 10
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1
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1.3k
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 14.6 years ago by 68k • written 14.6 years ago by ★ 1.5k
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1
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1.3k
views
normalization problem
Normalization affy Normalization affy
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 10
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2
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1.1k
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RMA and combining probesets into entrez genes
affy affy
updated 14.6 years ago by ▴ 160 • written 14.6 years ago by ▴ 40
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1
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3.1k
views
limma topTable annotation
GO hgu133plus2 affy limma convert Category GO hgu133plus2 affy limma convert Category
updated 14.7 years ago by ▴ 130 • written 14.7 years ago by 53k
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989
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limma topTable annotation
GO hgu133plus2 affy limma convert GO hgu133plus2 affy limma convert
updated 14.7 years ago by 68k • written 14.7 years ago by ▴ 130
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1.1k
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How to make a probe package with the GPL1073.probe file from GEO.
cdf probe affy convert AnnotationDbi cdf probe affy convert AnnotationDbi
updated 14.7 years ago by ★ 4.1k • written 14.7 years ago by ▴ 10
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1.2k
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Using annotation package how can I convert the probe > ID's to Gene names.
Annotation GO probe affy convert Annotation GO probe affy convert
14.8 years ago Paul Geeleher ★ 1.3k
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6
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1.9k
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Unable to Generate QC Report for mogene10stv1
Annotation GO GUI affy PROcess affyQCReport Annotation GO GUI affy PROcess affyQCReport
updated 14.8 years ago by 68k • written 14.8 years ago by ▴ 110
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1.2k
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question about get a summary gene expression information from the probe set associated with one specific gene
Annotation GO cdf probe affy convert ASSIGN Annotation GO cdf probe affy convert
updated 14.8 years ago by ▴ 90 • written 14.8 years ago by 68k
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1.1k
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affymetrix annotation
Annotation mouse4302 affy Annotation mouse4302 affy
14.8 years ago arne.mueller@novartis.com ▴ 200
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6
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2.0k
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affymetrix annotation
mouse4302 affy mouse4302 affy
updated 14.8 years ago by ▴ 250 • written 14.8 years ago by ▴ 200
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1.8k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
14.8 years ago Roman ▴ 20
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1.0k
views
copy number/LOH for Affy 100K
affy affy
14.8 years ago array chip ▴ 420
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2
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2.0k
views
FW: PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 14.9 years ago by ▴ 120 • written 14.9 years ago by ▴ 10
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2
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2.1k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 14.9 years ago by ★ 4.3k • written 14.9 years ago by ▴ 120
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2
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1.5k
views
How do I set the median when performing MAS5.0 normalization
Normalization affy Normalization affy
updated 14.9 years ago by ▴ 60 • written 14.9 years ago by 68k
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1.5k
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Illumina CanineHD CNV & crlmm?
GO HapMap cdf affy crlmm GO HapMap cdf affy crlmm
14.9 years ago Matthew Ritchie ▴ 1000
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1
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2.1k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 20
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1.3k
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Illumina CanineHD CNV & crlmm?
GO cdf affy crlmm GO cdf affy crlmm
14.9 years ago Dykema, Karl ▴ 90
1,805 results • Page 9 of 37
Recent ...
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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