Showing : oligo • reset
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Oligo package and tiling arrays - PM and MM
cdf affyio oligo BufferedMatrix cdf affyio oligo BufferedMatrix
18.0 years ago Naira Naouar ▴ 140
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760
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About ndups error chol(V)
Microarray limma oligo Microarray limma oligo
18.1 years ago Gordon Smyth 53k
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makePDpackage: Problem loading PD package in, oligo:read.celfiles function
cdf oligo cdf oligo
18.1 years ago Matt Settles ▴ 10
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1
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1.1k
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request for simple usage of probe level normalisations
cdf gcrma oligo pdInfoBuilder cdf gcrma oligo pdInfoBuilder
updated 18.2 years ago by ★ 6.5k • written 18.2 years ago by ▴ 320
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5
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1.2k
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Making a PD package for Oligo
cdf oligo makePlatformDesign cdf oligo makePlatformDesign
updated 18.2 years ago by ★ 4.3k • written 18.2 years ago by ▴ 40
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1
reply
1.3k
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batch effects and VSN
Normalization Regression vsn limma oligo Normalization Regression vsn limma oligo
updated 18.2 years ago by ★ 13k • written 18.2 years ago by ▴ 330
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926
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Getting associated genes from SNP anntotation files
SNP oligo SNP oligo
18.2 years ago Holger Schwender ▴ 900
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1
reply
935
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appropriate statistical test for post-array analysis
probe oligo probe oligo
updated 18.3 years ago by ★ 6.0k • written 18.3 years ago by ▴ 100
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3
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1.9k
views
pd.mapping 10Karray
BiocViews cdf affyio biocViews oligo pdInfoBuilder BufferedMatrix BiocViews BiocViews cdf
updated 18.3 years ago by ★ 7.4k • written 18.3 years ago by ▴ 10
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Nimblegen analysis using oligo
oligo oligo
18.4 years ago Rene Dreos JIC ▴ 50
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1
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928
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Memory problems with the Oligo package
oligo oligo
updated 18.4 years ago by ★ 4.3k • written 18.4 years ago by ▴ 40
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4
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1.6k
views
SNPRMA: Normalizing...Error in readChar(con, 5) : cannot open the connection
oligo oligo
updated 18.5 years ago by ★ 4.3k • written 18.5 years ago by ▴ 50
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1
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874
views
Error in the Oligo package with pd.mapping50k.xba240
GUI oligo GUI oligo
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ▴ 40
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1
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905
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Documentation needed for Oligo package
oligo oligo
updated 18.5 years ago by ★ 4.3k • written 18.5 years ago by ▴ 40
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4
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1.9k
views
memory error on unix
oligo oligo
updated 18.5 years ago by ▴ 30 • written 18.5 years ago by ▴ 120
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0
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1.2k
views
Normalization of 2 color Nimblegen array
cdf affy affyPLM convert oligo makePlatformDesign cdf affy affyPLM convert oligo
18.5 years ago dhruv pant ▴ 30
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2
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1.7k
views
crlmm error: cluster centres
oligo oligo
updated 18.5 years ago by ★ 4.3k • written 18.5 years ago by ▴ 120
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3
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1.4k
views
Fwd: pmStrand() in oligo (version...)
SNP oligo SNP oligo
18.5 years ago Benilton Carvalho ★ 4.3k
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1
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1.3k
views
Problem with snprma
SNP Biobase oligo BufferedMatrix SNP Biobase oligo BufferedMatrix
updated 18.5 years ago by ★ 4.3k • written 18.5 years ago by ▴ 80
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2
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1.3k
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Nimblegen data analysis
GO cdf affy oligo GO cdf affy oligo
updated 18.6 years ago by ▴ 140 • written 18.6 years ago by ★ 2.2k
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Problem with customised endnode list in ontoCompare(goToolspackage)
Microarray GO graph goTools Category oligo Microarray GO graph goTools Category oligo
18.6 years ago Paquet, Agnes ▴ 500
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1.3k
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verification
GO limma impute oligo makePlatformDesign crlmm GO limma impute oligo makePlatformDesign
18.7 years ago Vasiliki Xiarchou ▴ 10
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8
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2.0k
views
crlmm warning
oligo crlmm oligo crlmm
updated 18.8 years ago by ★ 4.3k • written 18.8 years ago by ▴ 190
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0
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1.2k
views
Affymetrix promoter arrays
Normalization oligo Normalization oligo
18.8 years ago Jenny Drnevich ★ 2.2k
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1.2k
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question about the value retured by function ontoCompare()
GO hgu133a probe PROcess goTools oligo GO hgu133a probe PROcess goTools oligo
18.8 years ago Paquet, Agnes ▴ 500
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8
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2.3k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 18.8 years ago by ★ 7.4k • written 18.8 years ago by ★ 2.2k
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802
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makePDpackage for tiling arrays
oligo oligo
18.8 years ago Jenny Drnevich ★ 2.2k
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1
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868
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Finding peaks on tiling arrays/ moving average?
oligo oligo
updated 18.8 years ago by 21k • written 18.8 years ago by ★ 1.9k
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5
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1.7k
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Looking for R package for Nimblegen expression data
oligo makePlatformDesign oligo makePlatformDesign
18.8 years ago Xinxia Peng ▴ 120
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2
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1.6k
views
imputing missing data for 70mer array platform, need advice
aCGH CGH multtest impute aCGH oligo aCGH CGH multtest impute aCGH oligo
updated 18.9 years ago by 21k • written 18.9 years ago by ▴ 50
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3
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1.4k
views
saturated spots
limma oligo limma oligo
updated 18.9 years ago by ★ 1.9k • written 18.9 years ago by ▴ 330
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2
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1.3k
views
"oligo" crashes in windows XP
SNP GO affyio oligo crlmm SNP GO affyio oligo crlmm
updated 18.9 years ago by ★ 4.3k • written 18.9 years ago by ▴ 190
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1
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1.4k
views
goTools problem
goTools oligo goTools oligo
updated 18.9 years ago by ▴ 500 • written 18.9 years ago by ▴ 30
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6
replies
2.2k
views
Normalization between arrays for common reference, time course and direct two color designs
Normalization limma oligo Normalization limma oligo
19.0 years ago Jenny Drnevich ★ 2.2k
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4
replies
1.5k
views
VSN exclusion of probes
probe vsn oligo probe vsn oligo
updated 19.0 years ago by ★ 13k • written 19.0 years ago by ▴ 330
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735
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[Bioc-devel] I will succeed (hopefully) the installation of Bioconductor 2.0
probe affy oligo probe affy oligo
19.1 years ago Francois Pepin ★ 1.3k
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3
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1.7k
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Spatial Correction
SNP Normalization affy oligo SNP Normalization affy oligo
updated 19.1 years ago by ▴ 120 • written 19.1 years ago by ▴ 170
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1
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1.1k
views
makePlatformDesign error
affyio oligo makePlatformDesign affyio oligo makePlatformDesign
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 20
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1
reply
719
views
creating platformdesign affy_250k nsp
PROcess oligo PROcess oligo
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 70
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votes
1
reply
691
views
cdfenv files ATTN: James McDonald part II
oligo oligo
updated 19.2 years ago by 21k • written 19.2 years ago by ▴ 20
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1
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1.4k
views
athPkgBuilder data source
Annotation Pathways GO probe oligo Annotation Pathways GO probe oligo
updated 19.3 years ago by ▴ 250 • written 19.3 years ago by ▴ 870
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946
views
[Bioc-devel] Appropriate linear model analysis for microarray time course comparison
TimeCourse limma timecourse oligo TimeCourse limma timecourse oligo
19.5 years ago Sean Davis 21k
0
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1
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1.5k
views
reference design
limma limmaGUI oligo limma limmaGUI oligo
updated 19.6 years ago by ★ 6.0k • written 19.6 years ago by ▴ 30
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0
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1.5k
views
parameterization or contrast matrix?
limma limmaGUI oligo limma limmaGUI oligo
19.6 years ago bzzandrew@interfree.it ▴ 30
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865
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FW: Does combineAffyBatch of package matchprobes elimi nate the wrong probe sets?
Normalization probe oligo Normalization probe oligo
19.7 years ago Christian.Stratowa@vie.boehringer-ingel… ▴ 270
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0
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769
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FW: Does combineAffyBatch of package matchprobes eliminate the wrong probe sets?
Normalization probe oligo Normalization probe oligo
19.7 years ago Wolfgang Huber ★ 13k
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3
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2.1k
views
Timeseries loop design analysis using Limma or Maanova?
Bayesian Clustering TimeCourse timecourse oligo Bayesian Clustering TimeCourse timecourse
19.8 years ago Pete ▴ 70
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7
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2.1k
views
presence/absence call using oligo array?
Microarray oligo Microarray oligo
19.9 years ago xpeng ▴ 60
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1
reply
1.3k
views
AnnBuilder/ABPkgBuilder URL problem
Annotation GO AnnBuilder oligo Annotation GO AnnBuilder oligo
updated 20.0 years ago by ▴ 780 • written 20.0 years ago by ▴ 100
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0
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816
views
Fwd:decideTests nestedF
limma oligo limma oligo
20.0 years ago daniela.marconi@libero.it ▴ 100
430 results • Page 8 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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