Showing : Limma • reset
1
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4
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1.5k
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 23 months ago by 53k • written 24 months ago by ▴ 10
4
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3
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1.2k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 24 months ago by 53k • written 24 months ago by • 0
2
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3
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1.2k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 24 months ago by 68k • written 24 months ago by • 0
1
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2
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2.6k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.7 years ago by • 0
0
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2
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771
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
24 months ago Lily Cheang ▴ 10
1
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2
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1.1k
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Longitudinal analysis in Limma
limma
2.0 years ago COPD_Project • 0
2
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2
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1.3k
views
Using limma for controlling age variable
linearmodeling limma
2.0 years ago Matej • 0
4
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6
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1.8k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 24 months ago by 53k • written 2.0 years ago by • 0
0
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5
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2.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
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4
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1.3k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
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2
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868
views
Assess fit of variance prior
limma
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 30
2
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1
reply
663
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
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4
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1.9k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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3
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962
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
5
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2
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1.7k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
12
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5
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5.4k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
0
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0
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745
views
multipollutant models
statistics Regression r limma
2.2 years ago Jitendra ▴ 10
0
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3
replies
1.4k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.2 years ago Karthik • 0
1
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1
reply
787
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
3
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4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.2 years ago pl23 • 0
2
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4
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1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.2 years ago Tyler Sagendorf ▴ 10
1
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4
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1.6k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
0
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4
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1.5k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 months ago by 43k • written 2.3 years ago by • 0
0
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5
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1.5k
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 2.2 years ago by 53k • written 2.3 years ago by • 0
0
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5
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1.9k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.3 years ago dorota.komar • 0
0
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1
reply
870
views
Issue with weights in voomLmFit()
limma
updated 14 months ago by 53k • written 2.3 years ago by ▴ 170
2
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1
reply
1.6k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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7
replies
1.9k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.2 years ago by 53k • written 2.3 years ago by • 0
5
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3
replies
1.3k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 180
5
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9
replies
3.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 21 months ago by 53k • written 2.3 years ago by ▴ 10
0
votes
1
reply
867
views
''Model_Matrix'' error
DifferentialExpression limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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6
replies
3.9k
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 9.2 years ago by ▴ 10
0
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0
replies
588
views
Huge effect of a single sample on DEGs
limma
2.4 years ago • updated 2.3 years ago Jonathan ▴ 10
1
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1
reply
839
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
3
votes
3
replies
1.1k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
votes
3
replies
3.8k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.4 years ago Ethan Nguyen • 0
1
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2
replies
2.1k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.4 years ago petertam1343 • 0
0
votes
6
replies
1.6k
views
Help with model.matrix and creating the right contrast matrix for limma
limma
2.4 years ago • updated 2.1 years ago rober204 • 0
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.4 years ago by 53k • written 4.2 years ago by ▴ 340
4
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5
replies
1.7k
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 2.3 years ago by 53k • written 2.4 years ago by ▴ 10
3
votes
13
replies
2.4k
views
Timely differentially expressed genes
timecoursedata limma
2.4 years ago • updated 2.2 years ago triZZla • 0
0
votes
1
reply
877
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 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
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6
replies
1.7k
views
Limma dispersed distribution of log fold change
limma
written 2.4 years ago by • 0
1
vote
0
replies
926
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.4 years ago svlachavas ▴ 840
0
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2
replies
930
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.5 years ago by • 0
1
vote
3
replies
1.5k
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 2.4 years ago by 53k • written 2.5 years ago by • 0
5
votes
5
replies
1.7k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.5 years ago Jitendra ▴ 10
2
votes
5
replies
3.1k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
votes
3
replies
3.2k
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 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
6
votes
7
replies
1.6k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
4,230 results • Page 4 of 85
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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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