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4
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2
answers
87
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5 follow
2
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Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicatecorrelation rna-seq technical replicates biological replicates written 5 days ago by paul.alto • 40 • updated 14 hours ago by Aaron Lun • 25k
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1
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50
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1
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Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer limma isoform isoformswitchanalyzer written 6 days ago by asmita • 0 • updated 5 days ago by k.vitting.seerup • 100
6
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3
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98
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dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and manual
limma differential expression repeated measures variancepartition dream written 7 days ago by hermidalc • 0 • updated 6 days ago by Gordon Smyth ♦ 38k
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148
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Multiple samples per individual and unbalanced number of samples per individual: DE between groups still an ordinary two-group comparison?
limma edger deseq2 differential expression repeated measures written 9 days ago by hermidalc • 0
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Variance unstable after fitting to linear model with limma-voom pipeline
limma voom written 7 days ago by kentfung • 0
3
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1
answer
53
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1
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Can't get function plotExonJunc to work?
limma written 13 days ago by dleng • 0 • updated 8 days ago by Yunshun Chen • 490
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1
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59
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1
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Opening Illumina HT12 V3.0 Data from GEO
normalization limma geo written 12 days ago by FL512 • 0
2
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2
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138
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5 follow
2
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DeSeq2 Design (A-B)-(C-D)
limma deseq2 written 12 days ago by Jonathan.allen • 10 • updated 12 days ago by Gordon Smyth ♦ 38k
1
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2
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133
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancepartition dream written 3 months ago by Ben • 0 • updated 12 days ago by gabriel.hoffman • 70
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102
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1
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
rnaseq limma R differential expression tpm written 12 days ago by atakanekiz • 20 • updated 12 days ago by Steve Lianoglou ♦ 12k
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How to perform a differential expression analysis from TCGA file EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
cancer limma deseq2 written 13 days ago by KCLiv • 0 • updated 13 days ago by svlachavas • 740
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68
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1
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Pair-wise Limma Analysis with time series data and two levels (control and treatment)
microarray limma paired deg time series written 13 days ago by kawess • 0 • updated 13 days ago by Gordon Smyth ♦ 38k
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2
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146
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RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized data and CPM
limma edger written 13 days ago by li.zhaoz • 0 • updated 13 days ago by Gordon Smyth ♦ 38k
2
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1
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55
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1
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How adjusted p-values are calculated in limma
limma statistics R fdr transcriptomics written 14 days ago by Wuschel • 10 • updated 14 days ago by Gordon Smyth ♦ 38k
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97
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1
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts written 17 days ago by uridavid.akavia • 0 • updated 17 days ago by Gordon Smyth ♦ 38k
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1
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182
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1
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UnProducible error with goana and kegga function
limma goana kegga written 21 days ago by Ahdee • 40 • updated 21 days ago by Gordon Smyth ♦ 38k
1
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1
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1.3k
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8 follow
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design matrix with limma
limma written 10.1 years ago by Diya v • 20 • updated 26 days ago by kobayotay • 0
3
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1
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104
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1
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Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy limma piano written 27 days ago by abolfazl.nikakhtar • 0 • updated 27 days ago by James W. MacDonald ♦ 51k
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155
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Blocking term for nested design in limma
limma model.matrix mixed-effects written 28 days ago by Finn • 0
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1
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51
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1
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makeContrasts from limma overides "i" as a varible
limma written 29 days ago by olof.rundquist • 0 • updated 28 days ago by James W. MacDonald ♦ 51k
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1
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171
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8 follow
1
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Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch written 4 weeks ago by english.server • 20 • updated 29 days ago by Gordon Smyth ♦ 38k
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2
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77
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Subsetting a data frame generated by topTable() {limma}
microarray limma toptable written 29 days ago by Alexander Az. • 20 • updated 29 days ago by Gordon Smyth ♦ 38k
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Technical replicates using Limma (handling within-subject and between-subject factors)
limma technical replicate written 4 weeks ago by sh.kazempour94 • 10 • updated 4 weeks ago by Gordon Smyth ♦ 38k
5
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1
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96
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1
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AnnotationData Packages for Agilent microarrays
microarray annotation limma agilent .db written 4 weeks ago by Alexander Az. • 20 • updated 4 weeks ago by James W. MacDonald ♦ 51k
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FPM value and batch correction
limma deseq2 written 4 weeks ago by Emir • 0 • updated 4 weeks ago by Michael Love ♦ 25k
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