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using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.2 years ago by ★ 6.5k • written 11.2 years ago by 50k
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3
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5.6k
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limma design and contrast matrix for paired experiment
Microarray limma edgeR Microarray limma edgeR
11.4 years ago • updated 11.3 years ago Gordon Smyth 50k
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806
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detailed analysis process of Comparisons Both Between and Within Subjects of edgeR
PROcess edgeR PROcess edgeR
11.4 years ago Gordon Smyth 50k
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1
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1.5k
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Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?
limma edgeR limma edgeR
updated 11.4 years ago by ★ 7.9k • written 11.4 years ago by 50k
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2
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1.2k
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Help interpreting many contrasts in one contrast versus many individual contrast matrices
hgu133plus2 hgu133plus2
updated 11.5 years ago by ★ 2.0k • written 11.5 years ago by 50k
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2
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1.5k
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How to design matrix on edgeR to study genotype x environmental interaction
Sequencing miRNA Normalization edgeR Sequencing miRNA Normalization edgeR
11.5 years ago Gordon Smyth 50k
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2
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696
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limma: instances of highly variable paired ratios, but very small p-values
Cancer limma Cancer limma
updated 11.5 years ago by ▴ 20 • written 11.5 years ago by 50k
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803
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LIMMA: Help needed for limma analysis with a complex design
limma limma
11.5 years ago Gordon Smyth 50k
0
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0
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850
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DE in edgeR
edgeR edgeR
11.5 years ago Gordon Smyth 50k
0
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0
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609
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How to design matrix on edgeR to study genotype x environmental interaction
Sequencing edgeR Sequencing edgeR
11.6 years ago Gordon Smyth 50k
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2
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2.2k
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limma topTable doesn't work without replicates [was: Help with limma]
GO limma GO limma
updated 11.6 years ago by ▴ 40 • written 11.6 years ago by 50k
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0
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1.0k
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limma topTable doesn't work without replicates [was: Help with limma]
GO limma GO limma
11.6 years ago Gordon Smyth 50k
0
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0
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922
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EdgeR gof plot below line
edgeR edgeR
11.6 years ago Gordon Smyth 50k
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0
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753
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ANOVA in edgeR?
edgeR DESeq edgeR DESeq
11.6 years ago Gordon Smyth 50k
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2
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1.1k
views
Mentored Projects at Bioconductor
updated 11.7 years ago by ▴ 390 • written 11.7 years ago by 50k
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2
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1.0k
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Install devel version of edgeR
edgeR edgeR
11.7 years ago Gordon Smyth 50k
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0
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1.5k
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edgeR: confusing BCV plot
11.7 years ago Gordon Smyth 50k
0
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0
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707
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strange results with edgeR::goodTuring
Category edgeR Category edgeR
11.7 years ago Gordon Smyth 50k
0
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8
replies
2.0k
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Limma normalization error and loess.R segmentation type fault (windows)
Normalization limma Normalization limma
11.7 years ago Gordon Smyth 50k
0
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8
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1.6k
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Variance stabilization of m-values
updated 11.7 years ago by ▴ 110 • written 11.8 years ago by 50k
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0
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813
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Can I adjust family relationship in Limma?
Microarray graph limma Microarray graph limma
11.8 years ago Gordon Smyth 50k
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0
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833
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(no subject)
Clustering probe limma GLAD Clustering probe limma GLAD
11.8 years ago Gordon Smyth 50k
0
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0
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728
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edgeR, error in estimateCommonDisp
edgeR edgeR
11.8 years ago Gordon Smyth 50k
0
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1
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857
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edgeR- data for case studies
SAGE PROcess edgeR SAGE PROcess edgeR
updated 11.8 years ago by ▴ 140 • written 11.8 years ago by 50k
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3
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1.2k
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edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 11.9 years ago by 25k • written 11.9 years ago by 50k
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0
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1.8k
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
11.9 years ago Gordon Smyth 50k
0
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0
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1.6k
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edge R design matrix pairwise comparison at different time points after infection with replicates
RNASeq Normalization edgeR RNASeq Normalization edgeR
11.9 years ago Gordon Smyth 50k
0
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0
replies
663
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Calculate the relation between mRNA and miRNA
miRNA miRNA
11.9 years ago Gordon Smyth 50k
0
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1
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1.4k
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reading single channel Agilent data with limma [was arrayQualityMetrics doesn't work...]
affy limma arrayQualityMetrics affy limma arrayQualityMetrics
updated 11.9 years ago by ★ 13k • written 11.9 years ago by 50k
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1
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4.2k
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File format for single channel analysis of Agilent microarray data with Limma?
Microarray probe Microarray probe
updated 12.0 years ago by ▴ 40 • written 12.0 years ago by 50k
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1
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824
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Expt. design question on optimal number of replicates (in edgeR or elsewhere)
RNASeq Organism edgeR RNASeq Organism edgeR
updated 12.0 years ago by ▴ 210 • written 12.0 years ago by 50k
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0
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1.3k
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technical and biological replicates in the same Exprset - Agi4x44
Microarray Normalization Microarray Normalization
12.0 years ago Gordon Smyth 50k
0
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1
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933
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technical and biological replicates in the same Exprset - Agi4x44
Microarray Normalization Microarray Normalization
updated 12.0 years ago by ▴ 10 • written 12.0 years ago by 50k
0
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0
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594
views
How to open the edgeR Users Guide within R?
limma edgeR limma edgeR
12.0 years ago Gordon Smyth 50k
0
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0
replies
2.7k
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How do I find up and down regulated genes for each contrast in LIMMA?
limma limma
12.0 years ago Gordon Smyth 50k
0
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0
replies
928
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Design and not estimable coefficients
limma limma
12.1 years ago Gordon Smyth 50k
0
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0
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1.1k
views
Filtering Codes (analysing Agilent 8x60k using limma)
Normalization limma Normalization limma
12.1 years ago Gordon Smyth 50k
0
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1
reply
1.2k
views
nested factors in edgeR [was: something wrong with my design matrix in edgeR]
12.1 years ago Gordon Smyth 50k
0
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0
replies
682
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edgeR questions
edgeR edgeR
12.1 years ago Gordon Smyth 50k
0
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0
replies
502
views
Array weights in the 'removeBatchEffect' function?
Clustering limma Clustering limma
12.1 years ago Gordon Smyth 50k
0
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0
replies
891
views
question about edgeR and Poisson model: common dispersion is too low
edgeR edgeR
12.1 years ago Gordon Smyth 50k
0
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0
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1.7k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
12.1 years ago Gordon Smyth 50k
0
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0
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3.2k
views
edgeR: Specifying the "coef"-argument in glmLRT in a two factor study
edgeR edgeR
12.1 years ago Gordon Smyth 50k
0
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0
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729
views
Alert to developers about changes to edgeR
edgeR edgeR
12.2 years ago Gordon Smyth 50k
1
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2
replies
7.3k
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LIMMA - summarization of Illumina probes for same gene
probe affy limma beadarray probe affy limma beadarray
updated 12.2 years ago by ▴ 180 • written 12.2 years ago by 50k
0
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1
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998
views
Summarizing Single-channel Agilent data
GO limma GO limma
12.2 years ago Gordon Smyth 50k
0
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0
replies
635
views
Testing for differential expression variability with edgeR
edgeR edgeR
12.2 years ago Gordon Smyth 50k
0
votes
1
reply
2.3k
views
Estimating fold change from limma 'log2FC' using lumi
Microarray Normalization limma lumi Microarray Normalization limma lumi
updated 12.3 years ago by ▴ 30 • written 12.3 years ago by 50k
0
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1
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2.1k
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Using write.table with output from topTags [was: report a possible bug of edgeR]
edgeR edgeR
updated 12.3 years ago by ▴ 380 • written 12.3 years ago by 50k
1
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1
reply
2.6k
views
Adjusting removeBatchEffect from limma
limma
12.3 years ago • updated 3.5 years ago Gordon Smyth 50k
679 results • Page 3 of 14
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