Showing : Limma • reset
3
votes
2
replies
127
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 2 days ago by 48k • written 3 days ago by • 0
0
votes
0
replies
52
views
multipollutant models
statistics Regression r limma
4 days ago Jitendra ▴ 10
0
votes
3
replies
162
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
11 days ago • updated 3 days ago Karthik • 0
1
vote
1
reply
138
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 5 days ago by 41k • written 11 days ago by • 0
3
votes
4
replies
246
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
11 days ago • updated 9 days ago pl23 • 0
2
votes
4
replies
289
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
17 days ago Tyler Sagendorf ▴ 10
1
vote
4
replies
341
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
4 weeks ago Wending • 0
0
votes
2
replies
240
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
5 weeks ago Crystal571 • 0
0
votes
5
replies
520
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 4 days ago by 48k • written 5 weeks ago by • 0
0
votes
5
replies
519
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
7 weeks ago • updated 6 weeks ago dorota.komar • 0
0
votes
1
reply
264
views
Issue with weights in voomLmFit()
limma
updated 7 weeks ago by 48k • written 7 weeks ago by ▴ 90
2
votes
1
reply
598
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 7 weeks ago by 48k • written 7 weeks ago by • 0
1
vote
4
replies
378
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 7 weeks ago by 48k • written 7 weeks ago by • 0
5
votes
3
replies
462
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 7 weeks ago by 48k • written 7 weeks ago by ▴ 180
5
votes
8
replies
627
views
Batch correction and repeated measures
RUVSeq sva limma
written 9 weeks ago by ▴ 10
0
votes
1
reply
233
views
''Model_Matrix'' error
DifferentialExpression limma
updated 10 weeks ago by 48k • written 10 weeks ago by • 0
1
vote
6
replies
2.3k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.0 years ago by ▴ 10
0
votes
0
replies
210
views
Huge effect of a single sample on DEGs
limma
10 weeks ago • updated 9 weeks ago Jonathan ▴ 10
1
vote
1
reply
197
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 10 weeks ago by 64k • written 10 weeks ago by ▴ 10
3
votes
3
replies
339
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 10 weeks ago by 64k • written 10 weeks ago by • 0
3
votes
3
replies
636
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
10 weeks ago Ethan Nguyen • 0
1
vote
2
replies
298
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
10 weeks ago petertam1343 • 0
0
votes
5
replies
441
views
Help with model.matrix and creating the right contrast matrix for limma
limma
updated 3 days ago by 48k • written 11 weeks ago by • 0
5
votes
5
replies
4.5k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 11 weeks ago by 48k • written 2.1 years ago by ▴ 330
4
votes
5
replies
610
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 9 weeks ago by 48k • written 11 weeks ago by ▴ 10
3
votes
13
replies
877
views
Timely differentially expressed genes
timecoursedata limma
12 weeks ago • updated 5 days ago triZZla • 0
0
votes
1
reply
315
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 3 months ago by ★ 3.6k • written 3 months ago by • 0
1
vote
6
replies
513
views
Limma dispersed distribution of log fold change
limma
written 3 months ago by • 0
1
vote
0
replies
322
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
3 months ago svlachavas ▴ 820
0
votes
2
replies
321
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 3 months ago by • 0
1
vote
3
replies
386
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 3 months ago by 48k • written 3 months ago by • 0
5
votes
5
replies
485
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
3 months ago Jitendra ▴ 10
2
votes
5
replies
634
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 3 months ago by 48k • written 3 months ago by • 0
1
vote
3
replies
413
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 3 months ago by 64k • written 3 months ago by • 0
5
votes
7
replies
468
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 4 months ago by 48k • written 4 months ago by ▴ 10
1
vote
2
replies
447
views
loading scores using plotMDS in limma
plotMDS limma
4 months ago • updated 3 months ago Cen • 0
2
votes
1
reply
405
views
Grouping DEGs yields varying results
RNASeq limma
updated 4 months ago by 48k • written 4 months ago by ▴ 10
0
votes
6
replies
535
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
2
replies
386
views
Fluidigm Data Batch Correction
sva limma
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
2
replies
359
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
4 months ago Eleonora • 0
3
votes
2
replies
326
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 4 months ago by 48k • written 4 months ago by • 0
1
vote
1
reply
475
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
4
replies
402
views
Pairwise comparison for DEG analysis
limma
updated 4 months ago by ★ 3.6k • written 4 months ago by • 0
3
votes
2
replies
625
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 4 months ago by 48k • written 4 months ago by ▴ 10
1
vote
1
reply
323
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 4 months ago by 48k • written 5 months ago by • 0
3
votes
2
replies
472
views
PhD student
TMM limma
5 months ago Nisha • 0
1
vote
5
replies
710
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 4 months ago by 48k • written 5 months ago by • 0
1
vote
4
replies
540
views
Pairwise differential expression using limma
limma
5 months ago Melissa • 0
2
votes
3
replies
494
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
5 months ago amnahsiddiqa • 0
0
votes
2
replies
318
views
Visualization of absolute values after batch effect correction
limma
updated 5 months ago by ▴ 320 • written 5 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
Thanks James for your helpful response. This particular experimental set up is very common in iPSC studies, where multiple differentiations…
Comment: DESeq2 test for synergistic vs additive effects by Jay • 0
Why is TrtAB - TrtA - TrtB + Control "not really a thing"? i came to this forum answer when attempting to use EdgeR to answer a similar que…
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by R_Page • 0
Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.
Votes
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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