Showing : Oligo • reset
2
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GeneFeatureSet
oligo oligo
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 20
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1.5k
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Bioconductor Digest, Vol 119, Issue 1
Preprocessing Homo sapiens affy oligo RPA Preprocessing Homo sapiens affy oligo RPA
updated 12.9 years ago by ▴ 20 • written 12.9 years ago by ▴ 40
0
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6
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2.3k
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Bioc packages not working with R2.15.2?
Cancer oligo Cancer oligo
updated 13.0 years ago by ★ 4.3k • written 13.0 years ago by ▴ 170
0
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0
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Issue with Genome Graphs
Annotation simpleaffy oligo GenomeGraphs frma Annotation simpleaffy oligo GenomeGraphs
13.1 years ago Jeremy Ng ▴ 180
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0
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1.1k
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Nimblegen microarray MM8_60mer_expr
Microarray Annotation oligo pdInfoBuilder Microarray Annotation oligo pdInfoBuilder
13.1 years ago Benilton Carvalho ★ 4.3k
0
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1
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1.9k
views
Difference number of probesets after RMA with Oligo package and APT
oligo oligo
updated 13.1 years ago by ★ 1.3k • written 13.1 years ago by ▴ 40
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1.1k
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Difference number of probesets after RMA with Oligo package and APT
oligo oligo
13.1 years ago Benilton Carvalho ▴ 50
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3
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1.6k
views
segfault during rma using oligo on Nimblegen data
oligo oligo
updated 13.1 years ago by ★ 4.3k • written 13.1 years ago by ▴ 30
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1.2k
views
help ith GeneAnswers / annotation package
Annotation GO oligo GeneAnswers Annotation GO oligo GeneAnswers
13.1 years ago Ingrid Mercier ▴ 60
0
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1
reply
2.4k
views
R matrix size limits and array data
oligo oligo
updated 13.1 years ago by ★ 4.3k • written 13.1 years ago by ▴ 230
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0
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869
views
rma and brightness of exon arrays
oligo oligo
13.1 years ago Rob Dunne ▴ 230
0
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2
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899
views
coefs<-getAffinitySplineCoefficients...design error message help
oligo oligo
updated 13.2 years ago by ★ 4.3k • written 13.2 years ago by ★ 13k
0
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2
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2.1k
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differences among pd.mogene.1.0.st.v1, mogene10sttranscriptcluster.db and mogene10stprobeset.db
Annotation oligo Annotation oligo
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 840
3
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4
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2.2k
views
cause 'memory not mapped' when use oligo
oligo oligoClasses oligo oligoClasses
updated 13.2 years ago by ▴ 50 • written 13.2 years ago by ★ 1.3k
1
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5
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views
paCalls oligo package
Transcription oligo Transcription oligo
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 190
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0
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1.2k
views
Affymetrix gene st array - ok to do statistics on Category:Main only?
limma plier oligo limma plier oligo
13.3 years ago Martin O'Hare ▴ 10
0
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2.8k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization probe oligo frma frmaTools Normalization probe oligo frma frmaTools
13.3 years ago Schott, Johanna ▴ 20
0
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3
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1.3k
views
Oligo package, possible bug in paCalls
oligo oligo
updated 13.4 years ago by ★ 4.3k • written 13.4 years ago by ▴ 120
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1
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1.3k
views
oligo: ordering of \"backgroundCorrect\" and \"normalize\" output values
Normalization Preprocessing probe oligo Normalization Preprocessing probe oligo
updated 13.4 years ago by ★ 4.3k • written 13.4 years ago by ★ 13k
0
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1.5k
views
boxplot/histograms on preprocessed SNP affy data with crlmm package
SNP oligo crlmm SNP oligo crlmm
updated 13.5 years ago by ★ 4.3k • written 13.5 years ago by ▴ 840
0
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1
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1.3k
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oligo: error in crlmm function
SNP oligo SNP oligo
updated 13.5 years ago by ★ 4.3k • written 13.5 years ago by ▴ 840
0
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2
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1.6k
views
oligo and pdInfoBuilder
Annotation Yeast oligo pdInfoBuilder Annotation Yeast oligo pdInfoBuilder
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 340
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3
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3.5k
views
GWAS with Affymetrix SNP 6.0
SNP oligo snpMatrix snpStats SNP oligo snpMatrix snpStats
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 20
0
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1
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1.6k
views
Using BrainArray mappings with oligo package
Annotation cdf oligo Annotation cdf oligo
updated 13.5 years ago by ★ 4.3k • written 13.5 years ago by ▴ 600
0
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3
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2.2k
views
How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Microarray Annotation Normalization GO probe genefilter affy limma oligo Microarray GO
updated 13.6 years ago by ▴ 190 • written 13.6 years ago by 68k
0
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1
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1.4k
views
How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Microarray Normalization probe genefilter limma oligo Microarray Normalization probe
updated 13.6 years ago by 68k • written 13.6 years ago by ▴ 190
0
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0
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Normalized values in oligo::crlmm and oligo::snprma don't match?
SNP Normalization oligo crlmm SNP Normalization oligo crlmm
13.6 years ago Denise Mak ▴ 10
0
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4
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4.3k
views
exprs() in Bioc 2.10
probe affy oligo probe affy oligo
updated 13.6 years ago by ★ 4.3k • written 13.6 years ago by ▴ 30
0
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2
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1.7k
views
oligo package: extracting position, sequence, and intensity from Affymetrix tiling array
BiocViews Organism biocViews oligo pdInfoBuilder BiocViews BiocViews Organism biocViews
updated 13.7 years ago by ★ 4.3k • written 13.7 years ago by ★ 13k
0
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2
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1.8k
views
pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays
Annotation oligo pdInfoBuilder oligoClasses Annotation oligo pdInfoBuilder oligoClasses
updated 13.7 years ago by ★ 4.3k • written 13.7 years ago by ▴ 630
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935
views
(no subject)
biomaRt oligo xmapcore biomaRt oligo xmapcore
13.7 years ago james perkins ▴ 300
0
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0
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1.5k
views
Ensembl gene ids corresponding to affymetrix rat exon array transcript level ids
biomaRt oligo biomaRt oligo
13.7 years ago James Perkins ▴ 120
0
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1
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1.7k
views
GO Analysis for Mouse Exon Array
Annotation Pathways GO limma GOstats oligo Annotation Pathways GO limma GOstats oligo
updated 13.8 years ago by ★ 4.3k • written 13.8 years ago by ▴ 60
0
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2
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1.5k
views
affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Microarray cdf affy makecdfenv PROcess oligo cycle Microarray cdf affy makecdfenv oligo
updated 13.9 years ago by 68k • written 13.9 years ago by ▴ 630
0
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1
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920
views
How remove controls probes - Affymetrix Gene
GO probe oligo GO probe oligo
updated 13.9 years ago by 68k • written 13.9 years ago by ★ 13k
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1.7k
views
limma - 2-color agilent microarray, GO annotation
Microarray Annotation GO Organism limma GOstats oligo ASSIGN Microarray Annotation GO
13.9 years ago Gordon Smyth 53k
0
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1.2k
views
Bioconductor Digest, Vol 106, Issue 21
SNP Microarray VariantAnnotation Annotation cdf probe affy limma PROcess oligo xps SNP
14.0 years ago Jing Huang ▴ 380
0
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1
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1.3k
views
limma - 2-color agilent microarray, GO annotation
Annotation GO annotate oligo Annotation GO annotate oligo
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 290
0
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3
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1.6k
views
Practical utilization of SQN in ST1.0 Gene normalization.
Bayesian Cancer oligo Bayesian Cancer oligo
updated 14.1 years ago by ★ 4.2k • written 14.1 years ago by ★ 2.0k
0
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0
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1.7k
views
NUSE and RLE PLOTS for ST1.0 Gene chips with oligo w/o 1st quantile line
Bayesian Cancer oligo Bayesian Cancer oligo
14.1 years ago Richard Friedman ★ 2.0k
0
votes
0
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943
views
Erros in crlmm Re: SNP 6 chip
SNP Sequencing affy oligo xps crlmm SNP Sequencing affy oligo xps crlmm
14.1 years ago Benilton Carvalho ★ 4.3k
3
votes
2
replies
1.6k
views
rma of oligo feature set crashes R
oligo oligo
updated 14.2 years ago by ★ 4.3k • written 14.2 years ago by ▴ 750
4
votes
5
replies
1.6k
views
error when running paCalls
oligo oligo
updated 14.2 years ago by ★ 6.8k • written 14.2 years ago by ▴ 30
0
votes
4
replies
2.5k
views
How to merge to two cel objects imported by oligo package
affy oligo affy oligo
updated 14.3 years ago by ★ 4.3k • written 14.3 years ago by ▴ 60
0
votes
2
replies
2.0k
views
Unable to read Affy Mouse Exon 1.0 ST array CEL file
Annotation cdf affy gcrma oligo Annotation cdf affy gcrma oligo
updated 14.3 years ago by ★ 3.9k • written 14.3 years ago by ▴ 60
0
votes
0
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790
views
Problem about extracting interest data from NimbleGen oligo array
Annotation Preprocessing oligo Annotation Preprocessing oligo
14.4 years ago Benilton Carvalho ★ 4.3k
0
votes
0
replies
628
views
Problem about R analysis of Nimblegen microarray data
Annotation oligo Annotation oligo
14.4 years ago 陈娟 ▴ 70
0
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0
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1.1k
views
limma design and contrast matrices for two-color (two-channel) data with common biological reference, not common mRNA reference
Microarray Organism limma oligo Microarray Organism limma oligo
14.4 years ago Chris Lasher ▴ 10
0
votes
2
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1.6k
views
Affymetrix Gene Chip Normalization
Normalization affy oligo xps Normalization affy oligo xps
updated 14.5 years ago by ★ 3.9k • written 14.5 years ago by ▴ 30
0
votes
0
replies
1.8k
views
Using pdInfoBuilder for Human Exon Array
BiocViews Annotation Organism cdf biocViews oligo pdInfoBuilder BiocViews BiocViews cdf
14.5 years ago Maria Rodrigo-Domingo / Region Nordjyll… ▴ 10
430 results • Page 5 of 9
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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