Showing : Limma • reset
3
votes
2
replies
88
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 22 hours ago by 48k • written 1 day ago by • 0
0
votes
0
replies
38
views
multipollutant models
statistics Regression r limma
2 days ago Jitendra ▴ 10
0
votes
3
replies
140
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
9 days ago • updated 1 day ago Karthik • 0
1
vote
1
reply
131
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 3 days ago by 41k • written 9 days ago by • 0
3
votes
4
replies
234
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
9 days ago • updated 7 days ago pl23 • 0
2
votes
4
replies
283
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
15 days ago • updated 14 days ago Tyler Sagendorf ▴ 10
1
vote
4
replies
337
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
29 days ago • updated 28 days ago Wending • 0
0
votes
2
replies
233
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
5 weeks ago Crystal571 • 0
0
votes
5
replies
496
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 2 days ago by 48k • written 5 weeks ago by • 0
0
votes
5
replies
510
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
261
views
Issue with weights in voomLmFit()
limma
updated 6 weeks ago by 48k • written 7 weeks ago by ▴ 90
2
votes
1
reply
595
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
374
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
457
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
620
views
Batch correction and repeated measures
RUVSeq sva limma
written 9 weeks ago by ▴ 10
0
votes
1
reply
229
views
''Model_Matrix'' error
DifferentialExpression limma
updated 9 weeks ago by 48k • written 9 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
207
views
Huge effect of a single sample on DEGs
limma
10 weeks ago • updated 9 weeks ago Jonathan ▴ 10
1
vote
1
reply
193
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
332
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
628
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
293
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
10 weeks ago petertam1343 • 0
0
votes
5
replies
432
views
Help with model.matrix and creating the right contrast matrix for limma
limma
updated 1 day 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
603
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
854
views
Timely differentially expressed genes
timecoursedata limma
12 weeks ago • updated 3 days ago triZZla • 0
0
votes
1
reply
310
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
505
views
Limma dispersed distribution of log fold change
limma
written 3 months ago by • 0
1
vote
0
replies
320
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
318
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
383
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
481
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
3 months ago Jitendra ▴ 10
2
votes
5
replies
624
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
410
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
462
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
439
views
loading scores using plotMDS in limma
plotMDS limma
4 months ago • updated 3 months ago Cen • 0
2
votes
1
reply
402
views
Grouping DEGs yields varying results
RNASeq limma
updated 4 months ago by 48k • written 4 months ago by ▴ 10
0
votes
6
replies
531
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
381
views
Fluidigm Data Batch Correction
sva limma
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
2
replies
357
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
4 months ago Eleonora • 0
3
votes
2
replies
322
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
469
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
397
views
Pairwise comparison for DEG analysis
limma
updated 4 months ago by ★ 3.6k • written 4 months ago by • 0
3
votes
2
replies
620
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
321
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 4 months ago by 48k • written 4 months ago by • 0
3
votes
2
replies
468
views
PhD student
TMM limma
4 months ago Nisha • 0
1
vote
5
replies
706
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
538
views
Pairwise differential expression using limma
limma
5 months ago Melissa • 0
2
votes
3
replies
490
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
312
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: Why is DMRcate not available for Bioconductor version 3.18? by Daniel E. Weeks ▴ 20
Thank you for the explanation and contacting the DSS package authors.
Comment: Why is DMRcate not available for Bioconductor version 3.18? by shepherl 3.6k
The DSS package authors just need to add `edgeR` to their Suggest of their DESCRIPTION. They have been contacted about it but have not acte…
Answer: GOslim missing GO term by James W. MacDonald 64k
I think it's because that GO term isn't an offspring of any term in the GO slim you are downloading. ``` > ids<- "GO:0002831" > slim <…
Answer: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient by James W. MacDonald 64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Votes
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?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Awards • All
Scholar to James W. MacDonald 64k
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