Showing : marray • reset
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summarization for G4110B two colors agilent array: how to?
marray agilent twochannel normalization limma
updated 10.9 years ago by 53k • written 10.9 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
12.1 years ago Scott Robinson ▴ 130
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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 12.2 years ago by ★ 3.9k • written 12.2 years ago by ★ 13k
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Package/Function for Single Channel Microarray Spatial Normalization?
marray OLIN marray OLIN
12.3 years ago Guest User ★ 13k
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1
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2.1k
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How to subtract the background from foreground values in GenePix files
Normalization limma marray Normalization limma marray
updated 12.3 years ago by 68k • written 12.3 years ago by ★ 13k
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3
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Normalize background on marray Agilent object
Normalization limma PROcess marray Normalization limma PROcess marray
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 50
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3
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1.8k
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Normalize background on marray Agilent object
marray marray
12.4 years ago Guillermo Marco Puche ▴ 50
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1.2k
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Agilent Dual channel array input & marray
marray marray
12.5 years ago Guillermo Marco Puche ▴ 50
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1
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1.5k
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Unexpected output from Limma background subtraction & Normalization
Microarray Normalization limma marray puma Microarray Normalization limma marray puma
updated 4.8 years ago by 53k • written 12.6 years ago by ▴ 20
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1
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1.4k
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Unexpected Results from Limma background subtraction & marray normalizatoin
Microarray Normalization limma marray Microarray Normalization limma marray
updated 4.8 years ago by 53k • written 12.6 years ago by ▴ 20
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NAs introduced by marrayNorm after background subtraction with Limma
Normalization probe limma marray Normalization probe limma marray
12.6 years ago Guest User ★ 13k
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normalizing two-color Agilent data from GEO...
marray marray
13.2 years ago Alan Derr ▴ 50
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1
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2.4k
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Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ★ 13k
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Error with read.SMD() of marray
marray marray
14.1 years ago Guest User ★ 13k
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load single-channel microarray
marray marray
14.2 years ago Paz Tapia Ramirez ▴ 150
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2
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1.4k
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M values; and dist functions
marray marray
updated 14.6 years ago by ★ 13k • written 14.6 years ago by ▴ 560
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2
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gcrma - u133aaofav2probe error
Microarray gcrma marray Microarray gcrma marray
updated 14.7 years ago by 68k • written 14.7 years ago by ▴ 10
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2
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Error in Heatmap: Could not find function "heatmap.2"
PROcess marray PROcess marray
updated 15.3 years ago by ▴ 830 • written 15.3 years ago by ▴ 40
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maPalette() and the number of colors returned (bug?)
marray marray
15.5 years ago Ali Tofigh ▴ 30
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1
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1.3k
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Could I use "genefilter" package for MArray data ?
genefilter limma marray genefilter limma marray
updated 15.6 years ago by ★ 13k • written 15.6 years ago by ▴ 230
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MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
15.7 years ago Gordon Smyth 53k
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11
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Issue with limma and normalization of Agilent data generated with a 20-bit scan
Normalization limma marray Normalization limma marray
updated 15.7 years ago by 53k • written 15.7 years ago by ▴ 130
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1.7k
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Bug in vsn2
limma marray limma marray
updated 16.4 years ago by ★ 13k • written 16.4 years ago by ▴ 50
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1.3k
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Summarization of cDNA microarray data
marray marray
updated 16.7 years ago by 21k • written 16.7 years ago by ▴ 10
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1
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1.3k
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Agilent miRNA
miRNA marray miRNA marray
updated 16.7 years ago by ▴ 40 • written 16.7 years ago by ▴ 200
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1.3k
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problems with marray and gpr files
marray marray
updated 16.9 years ago by 25k • written 16.9 years ago by ▴ 40
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Moe430A and Moe430B join
moe430a moe430b mouse4302 gcrma marray moe430a moe430b mouse4302 gcrma marray
17.4 years ago Matyas Flemr ▴ 10
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limma and marray data import problem
Microarray Normalization limma PROcess marray Microarray Normalization limma PROcess
updated 17.5 years ago by 53k • written 17.5 years ago by ▴ 90
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Fwd: Question about normalizing one color Agilent array using loess
Microarray Genetics Normalization limma marray Microarray Genetics Normalization limma
updated 17.5 years ago by ★ 13k • written 17.6 years ago by ▴ 30
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1.2k
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Input to vsn or limma of genepix file missing 635 columns
Annotation Normalization Biobase affy vsn limma marray convert Annotation Normalization
updated 17.6 years ago by ▴ 30 • written 17.6 years ago by 53k
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How to read a data.frame into limma or marray
Microarray Normalization limma marray Microarray Normalization limma marray
updated 18.0 years ago by ▴ 450 • written 18.0 years ago by ▴ 160
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800
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One directional spatial normalisation for microarray data
marray marray
updated 18.0 years ago by ★ 2.4k • written 18.0 years ago by ★ 3.4k
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3
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1.8k
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tweaks for the heatmap ()?
Clustering marray Clustering marray
updated 18.1 years ago by ▴ 510 • written 18.1 years ago by ▴ 270
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4
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1.7k
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Agilent CGH data
CGH arrayQuality marray CGH arrayQuality marray
updated 18.2 years ago by 21k • written 18.2 years ago by ▴ 230
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1.4k
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DNAcopy package, craeting CNA object
CGH marray DNAcopy CGH marray DNAcopy
updated 18.2 years ago by 21k • written 18.2 years ago by ▴ 230
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1.3k
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creating a copy number array data object in DNA copy
GO marray GO marray
updated 18.2 years ago by 68k • written 18.2 years ago by ▴ 230
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8
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Reading Agilent files using read.maimages
Survival DynDoc genefilter tkWidgets affy vsn marray convert ArrayExpress Survival affy
updated 18.3 years ago by ▴ 20 • written 18.3 years ago by ▴ 100
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RE : create an new AnnotatedDataFrame
Annotation Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio
updated 18.3 years ago by 25k • written 18.3 years ago by ▴ 30
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2.1k
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create an new AnnotatedDataFrame
Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio Survival
updated 18.3 years ago by 25k • written 18.3 years ago by ▴ 30
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2
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1.6k
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Error with arrayQuality
Microarray Cancer hexbin limma marray convert Microarray Cancer hexbin limma marray
updated 18.4 years ago by ★ 7.4k • written 18.4 years ago by ▴ 50
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1
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1.4k
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marray layout
Microarray marray Microarray marray
updated 18.4 years ago by ▴ 130 • written 18.4 years ago by ▴ 40
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1
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1.5k
views
tcl/tk and biocLite
Genetics Cancer tkWidgets widgetTools marray Genetics Cancer tkWidgets widgetTools marray
updated 18.6 years ago by ★ 7.4k • written 18.6 years ago by ▴ 30
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1.2k
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tcl/tk dependency of biocLite
Genetics Cancer tkWidgets widgetTools marray Genetics Cancer tkWidgets widgetTools marray
18.6 years ago grischa tödt ▴ 30
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1.1k
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marray and limma error with lmFit
Microarray limma marray Microarray limma marray
18.6 years ago Gordon Smyth 53k
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0
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1.4k
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marray and limma error with lmFit
Microarray Biobase DynDoc widgetTools limma arrayQuality marray convert Microarray DynDoc
18.6 years ago Paquet, Agnes ▴ 500
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2
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1.9k
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marray: problems loading genepix-files
marray marray
updated 18.7 years ago by ▴ 130 • written 18.7 years ago by ▴ 310
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1
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1.4k
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Help with GenePix files
Normalization marray GLAD Normalization marray GLAD
updated 18.7 years ago by ★ 7.4k • written 18.7 years ago by ▴ 310
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0
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1.6k
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marray and limma error with lmFit
limma marray limma marray
18.7 years ago Gordon Smyth 53k
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0
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1.3k
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normalizeBetweenArrays gives an error
Normalization marray convert Normalization marray convert
19.1 years ago Gordon Smyth 53k
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1.2k
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problems reading Illumina files using BeadExplorer
affy widgetTools limma marray convert affyio BeadExplorer affy widgetTools limma marray
19.1 years ago Vitalina Komashko ▴ 10
135 results • Page 1 of 3
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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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