Showing : marray • reset
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Unexpected Results from Limma background subtraction & marray normalizatoin
Microarray Normalization limma marray Microarray Normalization limma marray
updated 23 months ago by 47k • written 9.8 years ago by ▴ 20
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926
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Unexpected output from Limma background subtraction & Normalization
Microarray Normalization limma marray puma Microarray Normalization limma marray puma
updated 23 months ago by 47k • written 9.8 years ago by ▴ 20
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1.8k
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summarization for G4110B two colors agilent array: how to?
marray agilent twochannel normalization limma
updated 8.0 years ago by 47k • written 8.0 years ago by ▴ 240
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How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization hu6800 affy gcrma marray nnNorm Harshlight Microarray hu6800
9.3 years ago Scott Robinson ▴ 130
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6
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1.2k
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How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization affy marray nnNorm Microarray Normalization affy marray nnNorm
updated 9.4 years ago by ★ 3.9k • written 9.4 years ago by ★ 12k
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Package/Function for Single Channel Microarray Spatial Normalization?
marray OLIN marray OLIN
9.4 years ago Guest User ★ 12k
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1
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1.5k
views
How to subtract the background from foreground values in GenePix files
Normalization limma marray Normalization limma marray
updated 9.5 years ago by 62k • written 9.5 years ago by ★ 12k
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3
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996
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Normalize background on marray Agilent object
Normalization limma PROcess marray Normalization limma PROcess marray
updated 9.5 years ago by 47k • written 9.6 years ago by ▴ 50
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3
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1.2k
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Normalize background on marray Agilent object
marray marray
9.6 years ago Guillermo Marco Puche ▴ 50
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846
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Agilent Dual channel array input & marray
marray marray
9.7 years ago Guillermo Marco Puche ▴ 50
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0
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751
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NAs introduced by marrayNorm after background subtraction with Limma
Normalization probe limma marray Normalization probe limma marray
9.8 years ago Guest User ★ 12k
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1.0k
views
normalizing two-color Agilent data from GEO...
marray marray
10.3 years ago Alan Derr ▴ 50
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1
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1.7k
views
Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 10.9 years ago by 13k • written 10.9 years ago by ★ 12k
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863
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Error with read.SMD() of marray
marray marray
11.3 years ago Guest User ★ 12k
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740
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load single-channel microarray
marray marray
11.4 years ago Paz Tapia Ramirez ▴ 150
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2
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846
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M values; and dist functions
marray marray
updated 11.8 years ago by 13k • written 11.8 years ago by ▴ 560
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2
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1.2k
views
gcrma - u133aaofav2probe error
Microarray gcrma marray Microarray gcrma marray
updated 11.9 years ago by 62k • written 11.9 years ago by ▴ 10
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2
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4.6k
views
Error in Heatmap: Could not find function "heatmap.2"
PROcess marray PROcess marray
updated 12.5 years ago by ▴ 830 • written 12.5 years ago by ▴ 40
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704
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maPalette() and the number of colors returned (bug?)
marray marray
12.6 years ago Ali Tofigh ▴ 30
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1
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864
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Could I use "genefilter" package for MArray data ?
genefilter limma marray genefilter limma marray
updated 12.8 years ago by 13k • written 12.8 years ago by ▴ 230
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665
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MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
12.9 years ago Gordon Smyth 47k
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11
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1.3k
views
Issue with limma and normalization of Agilent data generated with a 20-bit scan
Normalization limma marray Normalization limma marray
updated 12.9 years ago by 47k • written 12.9 years ago by ▴ 130
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1
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1.1k
views
Bug in vsn2
limma marray limma marray
updated 13.5 years ago by 13k • written 13.5 years ago by ▴ 50
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1
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826
views
Summarization of cDNA microarray data
marray marray
updated 13.8 years ago by 21k • written 13.8 years ago by ▴ 10
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1
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885
views
Agilent miRNA
miRNA marray miRNA marray
updated 13.9 years ago by ▴ 40 • written 13.9 years ago by ▴ 200
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1
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885
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problems with marray and gpr files
marray marray
updated 14.0 years ago by 25k • written 14.0 years ago by ▴ 40
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679
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Moe430A and Moe430B join
moe430a moe430b mouse4302 gcrma marray moe430a moe430b mouse4302 gcrma marray
14.5 years ago Matyas Flemr ▴ 10
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6
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1.3k
views
limma and marray data import problem
Microarray Normalization limma PROcess marray Microarray Normalization limma PROcess
updated 14.7 years ago by 47k • written 14.7 years ago by ▴ 90
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2
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1.0k
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Fwd: Question about normalizing one color Agilent array using loess
Microarray Genetics Normalization limma marray Microarray Genetics Normalization limma
updated 14.7 years ago by 13k • written 14.7 years ago by ▴ 30
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695
views
Input to vsn or limma of genepix file missing 635 columns
Annotation Normalization Biobase affy vsn limma marray convert Annotation Normalization
updated 14.7 years ago by ▴ 30 • written 14.7 years ago by 47k
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1.1k
views
How to read a data.frame into limma or marray
Microarray Normalization limma marray Microarray Normalization limma marray
updated 15.2 years ago by ▴ 450 • written 15.2 years ago by ▴ 160
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365
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One directional spatial normalisation for microarray data
marray marray
updated 15.2 years ago by ★ 2.4k • written 15.2 years ago by ★ 3.4k
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3
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1.1k
views
tweaks for the heatmap ()?
Clustering marray Clustering marray
updated 15.2 years ago by ▴ 510 • written 15.2 years ago by ▴ 270
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4
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922
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Agilent CGH data
CGH arrayQuality marray CGH arrayQuality marray
updated 15.3 years ago by 21k • written 15.3 years ago by ▴ 230
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1
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935
views
DNAcopy package, craeting CNA object
CGH marray DNAcopy CGH marray DNAcopy
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 230
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824
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creating a copy number array data object in DNA copy
GO marray GO marray
updated 15.4 years ago by 62k • written 15.4 years ago by ▴ 230
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8
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2.5k
views
Reading Agilent files using read.maimages
Survival DynDoc genefilter tkWidgets affy vsn marray convert ArrayExpress Survival affy
updated 15.5 years ago by ▴ 20 • written 15.5 years ago by ▴ 100
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2.3k
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RE : create an new AnnotatedDataFrame
Annotation Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 30
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1.3k
views
create an new AnnotatedDataFrame
Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio Survival
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 30
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2
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941
views
Error with arrayQuality
Microarray Cancer hexbin limma marray convert Microarray Cancer hexbin limma marray
updated 15.5 years ago by ★ 7.4k • written 15.5 years ago by ▴ 50
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1
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819
views
marray layout
Microarray marray Microarray marray
updated 15.6 years ago by ▴ 130 • written 15.6 years ago by ▴ 40
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1
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840
views
tcl/tk and biocLite
Genetics Cancer tkWidgets widgetTools marray Genetics Cancer tkWidgets widgetTools marray
updated 15.7 years ago by ★ 7.4k • written 15.7 years ago by ▴ 30
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0
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687
views
tcl/tk dependency of biocLite
Genetics Cancer tkWidgets widgetTools marray Genetics Cancer tkWidgets widgetTools marray
15.7 years ago grischa tödt ▴ 30
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0
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734
views
marray and limma error with lmFit
Microarray limma marray Microarray limma marray
15.8 years ago Gordon Smyth 47k
0
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0
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885
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marray and limma error with lmFit
Microarray Biobase DynDoc widgetTools limma arrayQuality marray convert Microarray DynDoc
15.8 years ago Paquet, Agnes ▴ 500
0
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2
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1.2k
views
marray: problems loading genepix-files
marray marray
updated 15.9 years ago by ▴ 130 • written 15.9 years ago by ▴ 310
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1
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872
views
Help with GenePix files
Normalization marray GLAD Normalization marray GLAD
updated 15.9 years ago by ★ 7.4k • written 15.9 years ago by ▴ 310
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0
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1.3k
views
marray and limma error with lmFit
limma marray limma marray
15.9 years ago Gordon Smyth 47k
0
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0
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716
views
normalizeBetweenArrays gives an error
Normalization marray convert Normalization marray convert
16.2 years ago Gordon Smyth 47k
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0
replies
761
views
problems reading Illumina files using BeadExplorer
affy widgetTools limma marray convert affyio BeadExplorer affy widgetTools limma marray
16.3 years ago Vitalina Komashko ▴ 10
50 results • Page 1 of 1
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Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot by Nathalie • 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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