Showing: limma • reset
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limma::avereps for median?
limma written 5 hours ago by b.nota • 340
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39
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Analyse Microarray Data - AVG_Signal
microarray limma written 12 hours ago by Alex Greenshields-Watson • 0
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Filtering lowly-expressed genes in a RNASeq dataset with continuous instead of grouping variables
limma edger written 7 days ago by anniina.mattila • 0 • updated 7 days ago by James W. MacDonald ♦ 51k
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67
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Account for inter individual variability at the baseline using nested models
limma edger written 14 days ago by Zeel • 0 • updated 14 days ago by Gordon Smyth ♦ 39k
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Limma analysis on a subset of data
limma written 15 days ago by chipolino • 0 • updated 15 days ago by Steve Lianoglou ♦ 12k
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2
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Error in write.fit step using limma package for microarray analysis
microarray limma written 18 days ago by sagayanilo • 0 • updated 15 days ago by James W. MacDonald ♦ 51k
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99
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batch effect correction for TCGA RNAseq harmonized data
limma deseq2 written 16 days ago by KCLiv • 10 • updated 15 days ago by Michael Love ♦ 26k
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1
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93
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Limma gives big p-values for large LFC
limma voom written 18 days ago by chipolino • 0 • updated 18 days ago by Gordon Smyth ♦ 39k
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Error in E-Eb Limma package
limma error e-eb written 18 days ago by diego.orihuelatacuri • 0 • updated 18 days ago by Gordon Smyth ♦ 39k
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Defining the design for a complicated multi-level experiment in Limma
rnaseq limma R voom written 19 days ago by Colari19 • 0 • updated 19 days ago by James W. MacDonald ♦ 51k
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DESeq2: design = ~1 For Normalisation Only.
rnaseq normalization limma deseq2 tcga written 21 days ago by Alex Greenshields-Watson • 0 • updated 21 days ago by Michael Love ♦ 26k
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7 follow
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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 4 weeks ago by paul.alto • 50 • updated 29 days ago by Aaron Lun • 25k
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Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer limma isoform isoformswitchanalyzer written 4 weeks ago by asmita • 0 • updated 4 weeks ago by k.vitting.seerup • 100
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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 5 weeks ago by hermidalc • 0 • updated 4 weeks ago by Gordon Smyth ♦ 39k
3
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195
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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 5 weeks ago by hermidalc • 0
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Variance unstable after fitting to linear model with limma-voom pipeline
limma voom written 5 weeks ago by kentfung • 0
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67
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Can't get function plotExonJunc to work?
limma written 5 weeks ago by dleng • 0 • updated 5 weeks ago by Yunshun Chen • 510
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1
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Opening Illumina HT12 V3.0 Data from GEO
normalization limma geo written 5 weeks ago by FL512 • 0
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5 follow
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DeSeq2 Design (A-B)-(C-D)
limma deseq2 written 5 weeks ago by Jonathan.allen • 10 • updated 5 weeks ago by Gordon Smyth ♦ 39k
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2
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170
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancepartition dream written 4 months ago by Ben • 0 • updated 5 weeks ago by gabriel.hoffman • 80
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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 5 weeks ago by atakanekiz • 30 • updated 5 weeks ago by Steve Lianoglou ♦ 12k
2
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How to perform a differential expression analysis from TCGA file EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
cancer limma deseq2 written 5 weeks ago by KCLiv • 10 • updated 5 weeks ago by svlachavas • 740
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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 6 weeks ago by kawess • 0 • updated 5 weeks ago by Gordon Smyth ♦ 39k
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RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized data and CPM
limma edger written 6 weeks ago by li.zhaoz • 0 • updated 5 weeks ago by Gordon Smyth ♦ 39k
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How adjusted p-values are calculated in limma
limma statistics R fdr transcriptomics written 6 weeks ago by Wuschel • 10 • updated 6 weeks ago by Gordon Smyth ♦ 39k
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