Showing : limma • reset
2
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2
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1.2k
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Using limma for controlling age variable
linearmodeling limma
21 months ago Matej • 0
4
votes
6
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1.6k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 21 months ago by 53k • written 22 months ago by • 0
0
votes
5
replies
1.9k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
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4
replies
1.2k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 22 months ago by 53k • written 23 months ago by • 0
1
vote
2
replies
825
views
Assess fit of variance prior
limma
updated 23 months ago by 53k • written 23 months ago by ▴ 30
2
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1
reply
627
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 23 months ago by 53k • written 23 months ago by • 0
2
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4
replies
1.8k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
3
replies
886
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 23 months ago by ▴ 360 • written 23 months ago by • 0
5
votes
2
replies
1.5k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 23 months ago by 53k • written 23 months ago by • 0
12
votes
5
replies
5.0k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by • 0 • written 23 months ago by • 0
0
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0
replies
691
views
multipollutant models
statistics Regression r limma
23 months ago Jitendra ▴ 10
0
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3
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1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
23 months ago Karthik • 0
1
vote
1
reply
722
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
3
votes
4
replies
1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
23 months ago pl23 • 0
2
votes
4
replies
1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
24 months ago Tyler Sagendorf ▴ 10
1
vote
4
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1.5k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.0 years ago Wending • 0
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 months ago by 43k • written 2.1 years ago by • 0
0
votes
5
replies
1.4k
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 23 months ago by 53k • written 2.1 years ago by • 0
0
votes
5
replies
1.8k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.1 years ago dorota.komar • 0
0
votes
1
reply
810
views
Issue with weights in voomLmFit()
limma
updated 12 months ago by 53k • written 2.1 years ago by ▴ 170
2
votes
1
reply
1.5k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
vote
7
replies
1.8k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 23 months ago by 53k • written 2.1 years ago by • 0
5
votes
3
replies
1.2k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 180
5
votes
9
replies
2.8k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 19 months ago by 53k • written 2.1 years ago by ▴ 10
0
votes
1
reply
823
views
''Model_Matrix'' error
DifferentialExpression limma
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
vote
6
replies
3.7k
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 9.0 years ago by ▴ 10
0
votes
0
replies
560
views
Huge effect of a single sample on DEGs
limma
2.1 years ago Jonathan ▴ 10
1
vote
1
reply
757
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
3
votes
3
replies
992
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
3
votes
3
replies
3.5k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.1 years ago Ethan Nguyen • 0
1
vote
2
replies
2.0k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.2 years ago • updated 2.1 years ago petertam1343 • 0
0
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6
replies
1.5k
views
Help with model.matrix and creating the right contrast matrix for limma
limma
2.2 years ago • updated 23 months ago rober204 • 0
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.2 years ago by 53k • written 4.0 years ago by ▴ 340
4
votes
5
replies
1.5k
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 2.1 years ago by 53k • written 2.2 years ago by ▴ 10
3
votes
13
replies
2.3k
views
Timely differentially expressed genes
timecoursedata limma
2.2 years ago • updated 23 months ago triZZla • 0
0
votes
1
reply
839
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 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
vote
6
replies
1.6k
views
Limma dispersed distribution of log fold change
limma
written 2.2 years ago by • 0
1
vote
0
replies
848
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.2 years ago svlachavas ▴ 840
0
votes
2
replies
883
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.2 years ago by • 0
1
vote
3
replies
1.4k
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
5
votes
5
replies
1.6k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.2 years ago Jitendra ▴ 10
2
votes
5
replies
2.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
votes
3
replies
3.0k
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 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
6
votes
7
replies
1.5k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.6k
views
loading scores using plotMDS in limma
plotMDS limma
2.3 years ago Cen • 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
0
votes
6
replies
1.4k
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
2
replies
1.2k
views
Fluidigm Data Batch Correction
sva limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
2
replies
1.2k
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.3 years ago Eleonora • 0
3
votes
2
replies
775
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
4,225 results • Page 4 of 85
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
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