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32
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0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray limma
19.6 years ago • updated 3.5 years ago Gordon Smyth 50k
5
votes
15
replies
1.7k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 4.6 years ago by 16k • written 4.6 years ago by 50k
1
vote
0
replies
1.5k
views
limma technical replicates and biological replicates in same design
limma SANTA
14.6 years ago • updated 4.8 years ago Gordon Smyth 50k
2
votes
0
replies
1.3k
views
Limma - decideTests - separate/nestedF questions
Microarray limma
17.0 years ago • updated 5.0 years ago Gordon Smyth 50k
8
votes
6
replies
2.5k
views
Compare and filter two BAM files, one record at a time
Rsamtools
updated 5.1 years ago by 25k • written 5.1 years ago by 50k
0
votes
1
reply
1.3k
views
Help on contrast matrix Limma
updated 5.3 years ago by 0 • written 14.6 years ago by 50k
5
votes
2
replies
2.9k
views
non-integer counts for edgeR
edgeR
11.9 years ago • updated 5.4 years ago Gordon Smyth 50k
0
votes
3
replies
4.1k
views
Use probesets with highest baseline expression for differential gene
Annotation probe limma
12.2 years ago • updated 5.6 years ago Gordon Smyth 50k
2
votes
3
replies
2.5k
views
org.Mm.eg.db gives wrong symbol for MT genes
org.mm.eg.db
10.7 years ago • updated 5.7 years ago Gordon Smyth 50k
1
vote
2
replies
2.3k
views
Columns used by read.maimages for Agilent arrays
Annotation CGH limma
11.7 years ago • updated 6.5 years ago Gordon Smyth 50k
6
votes
8
replies
2.2k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy aroma.affymetrix exon array xps oligo
6.8 years ago Gordon Smyth 50k
3
votes
4
replies
5.0k
views
LIMMA and Agilent single color
Annotation probe limma agilent
13.3 years ago • updated 7.3 years ago Gordon Smyth 50k
1
vote
0
replies
1.8k
views
DE analysis of PCR array [was: dataset dim for siggenes]
qPCR Normalization multtest limma siggenes
9.6 years ago • updated 7.3 years ago Gordon Smyth 50k
16
votes
0
replies
3.7k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
10.4 years ago • updated 7.9 years ago Gordon Smyth 50k
3
votes
2
replies
1.4k
views
Why does requireNamespace("org.Hs.eg.db") load DBI and RSQLite?
org.hs.eg.db DBI rsqlite
updated 8.0 years ago by 25k • written 8.0 years ago by 50k
6
votes
0
replies
2.8k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
17.7 years ago • updated 8.3 years ago Gordon Smyth 50k
0
votes
5
replies
4.6k
views
Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixe…
limma maanova rnaseq
10.8 years ago • updated 2.3 years ago Gordon Smyth 50k
1
vote
0
replies
998
views
Limma design: paired samples, batch effect
limma
15.1 years ago • updated 8.9 years ago Gordon Smyth 50k
0
votes
0
replies
816
views
general question about homogeneity of variances between microarray groups
Microarray limma
11.7 years ago • updated 8.9 years ago Gordon Smyth 50k
0
votes
0
replies
643
views
limma design for tech and biol replicates (1 color design)
limma
12.8 years ago • updated 9.2 years ago Gordon Smyth 50k
0
votes
0
replies
1.9k
views
edgeR: fold change reported by exactTest for zero values of rna-seq
edgeR
10.2 years ago • updated 9.3 years ago Gordon Smyth 50k
0
votes
0
replies
2.0k
views
Limma design matrix for time course experiment
affy limma
14.1 years ago • updated 9.3 years ago Gordon Smyth 50k
0
votes
0
replies
1.3k
views
Limma table results (time course analysis)
limma time course
10.0 years ago • updated 9.4 years ago Gordon Smyth 50k
0
votes
10
replies
1.8k
views
Interspecies differential expression of orthologs with Edger
Normalization Organism edgeR
updated 9.6 years ago by ▴ 140 • written 9.6 years ago by 50k
0
votes
0
replies
1.3k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing Alignment GO edgeR DESeq2 Sequencing Alignment GO edgeR DESeq2
9.6 years ago Gordon Smyth 50k
1
vote
0
replies
674
views
Combing Effects (t-stats) from experiment with common reference design?
9.6 years ago Gordon Smyth 50k
0
votes
1
reply
1.1k
views
multi-level design - a simplified question - corrected table
updated 9.7 years ago by ▴ 550 • written 9.7 years ago by 50k
0
votes
4
replies
646
views
time course experiment
updated 9.8 years ago by ▴ 550 • written 9.7 years ago by 50k
0
votes
0
replies
4.0k
views
cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing miRNA edgeR Sequencing miRNA edgeR
9.8 years ago Gordon Smyth 50k
0
votes
0
replies
1.4k
views
edgeR and DESeq2: model design and estimation of dispersion
limma edgeR DESeq2 limma edgeR DESeq2
9.8 years ago Gordon Smyth 50k
0
votes
2
replies
811
views
edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?
SAGE edgeR SAGE edgeR
9.9 years ago Gordon Smyth 50k
0
votes
2
replies
1.4k
views
Gene expression analysis with edgeR with a large, nested design matrix
edgeR edgeR
updated 9.9 years ago by ▴ 10 • written 9.9 years ago by 50k
0
votes
1
reply
916
views
limma all by all
Microarray limma Microarray limma
updated 9.9 years ago by ▴ 380 • written 9.9 years ago by 50k
0
votes
1
reply
1.4k
views
1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization
Normalization probe limma RankProd Normalization probe limma RankProd
updated 10.0 years ago by ▴ 30 • written 10.0 years ago by 50k
0
votes
1
reply
3.7k
views
total count filter cutoff (edgeR)
edgeR edgeR
10.0 years ago Gordon Smyth 50k
0
votes
0
replies
2.1k
views
EdgeR: dispersion estimation
edgeR edgeR
10.0 years ago Gordon Smyth 50k
0
votes
0
replies
3.7k
views
Interpretation of fold.changes for covariates in a linear model using voom
RNASeq RNASeq
10.0 years ago Gordon Smyth 50k
0
votes
1
reply
1.6k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by 50k
0
votes
0
replies
570
views
Join expression values of replicas in edgeR
Sequencing RNASeq edgeR Sequencing RNASeq edgeR
10.1 years ago Gordon Smyth 50k
0
votes
0
replies
1.1k
views
queries re Voom + Limma for RNA-seq data
Microarray Normalization GO limma Microarray Normalization GO limma
10.1 years ago Gordon Smyth 50k
0
votes
0
replies
1.5k
views
Handingly outliers with voom [was: tagwise parameters for negative binomial in edgeR]
limma limma
10.1 years ago Gordon Smyth 50k
1
vote
3
replies
1.7k
views
questions on edgeR package
RNASeq edgeR Rsubread RNASeq edgeR Rsubread
updated 10.2 years ago by ▴ 100 • written 10.2 years ago by 50k
0
votes
1
reply
772
views
Bioconductor Digest, Vol 132, Issue 5
PROcess edgeR PROcess edgeR
10.2 years ago Gordon Smyth 50k
0
votes
0
replies
1.0k
views
Identifying genes that contribute to limma's roast/romer gene set enrichments
10.2 years ago Gordon Smyth 50k
0
votes
10
replies
1.5k
views
EdgeR: artifacts on BCV plot
edgeR edgeR
10.2 years ago Gordon Smyth 50k
0
votes
0
replies
1.0k
views
EdgeR GOF plots
edgeR edgeR
10.2 years ago Gordon Smyth 50k
0
votes
0
replies
632
views
Best way of presenting a sub-fraction of edgeR RNAseq gene expression results in a publication
edgeR edgeR
10.2 years ago Gordon Smyth 50k
0
votes
2
replies
15k
views
EdgeR LogCpm and LogFC values calculation
edgeR edgeR
updated 10.2 years ago by ▴ 180 • written 10.2 years ago by 50k
0
votes
1
reply
2.0k
views
limma-voom
Normalization limma Normalization limma
updated 10.2 years ago by ▴ 380 • written 10.2 years ago by 50k
1
vote
4
replies
3.9k
views
pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
DESeq2
10.3 years ago • updated 21 months ago Gordon Smyth 50k
679 results • Page 1 of 14
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