Showing : Limma • reset
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removeBatchEffect with non-linear model fit
limma DESeq2
6 hours ago • updated 5 hours ago georgii.vdovin • 0
2
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4
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209
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 16 hours ago by 49k • written 2 days ago by • 0
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3
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138
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Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 1 day ago by ▴ 320 • written 1 day ago by • 0
1
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1
reply
104
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Asses fit of variance prior
limma
updated 2 days ago by 49k • written 3 days ago by ▴ 20
3
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2
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156
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 days ago by 49k • written 6 days ago by • 0
3
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2
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186
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 10 days ago by 49k • written 10 days ago by • 0
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0
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70
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multipollutant models
statistics Regression r limma
12 days ago Jitendra ▴ 10
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3
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196
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
19 days ago • updated 11 days ago Karthik • 0
1
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1
reply
153
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Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
3
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4
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271
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
18 days ago • updated 16 days ago pl23 • 0
2
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4
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317
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
25 days ago • updated 24 days ago Tyler Sagendorf ▴ 10
1
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4
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359
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 weeks ago Wending • 0
0
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2
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259
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
6 weeks ago Crystal571 • 0
0
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5
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556
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Limma continuous design (association polygenic risk score with gene expression)
limma
updated 12 days ago by 49k • written 7 weeks ago by • 0
0
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5
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550
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
8 weeks ago • updated 7 weeks ago dorota.komar • 0
0
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1
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276
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Issue with weights in voomLmFit()
limma
updated 8 weeks ago by 49k • written 8 weeks ago by ▴ 90
2
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1
reply
608
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 8 weeks ago by 49k • written 8 weeks ago by • 0
1
vote
7
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490
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 6 days ago by 49k • written 8 weeks ago by • 0
5
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3
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480
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 8 weeks ago by 49k • written 8 weeks ago by ▴ 180
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8
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664
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Batch correction and repeated measures
RUVSeq sva limma
written 10 weeks ago by ▴ 10
0
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1
reply
243
views
''Model_Matrix'' error
DifferentialExpression limma
updated 11 weeks ago by 49k • written 11 weeks ago by • 0
1
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6
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2.4k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.1 years ago by ▴ 10
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0
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216
views
Huge effect of a single sample on DEGs
limma
11 weeks ago • updated 10 weeks ago Jonathan ▴ 10
1
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1
reply
208
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Further analysis after limma regression output
statistics Epigenetics limma
updated 11 weeks ago by 64k • written 11 weeks ago by ▴ 10
3
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3
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357
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 11 weeks ago by 64k • written 11 weeks ago by • 0
3
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3
replies
665
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
11 weeks ago Ethan Nguyen • 0
1
vote
2
replies
318
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
12 weeks ago • updated 11 weeks ago petertam1343 • 0
0
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5
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474
views
Help with model.matrix and creating the right contrast matrix for limma
limma
updated 11 days ago by 49k • written 12 weeks ago by • 0
5
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5
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4.6k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 3 months ago by 49k • written 2.1 years ago by ▴ 330
4
votes
5
replies
630
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 10 weeks ago by 49k • written 3 months ago by ▴ 10
3
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13
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924
views
Timely differentially expressed genes
timecoursedata limma
3 months ago • updated 13 days ago triZZla • 0
0
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1
reply
325
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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
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6
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554
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Limma dispersed distribution of log fold change
limma
written 3 months ago by • 0
1
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0
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331
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
3 months ago svlachavas ▴ 820
0
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2
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330
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How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 3 months ago by • 0
1
vote
3
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403
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 3 months ago by 49k • written 3 months ago by • 0
5
votes
5
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517
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
3 months ago Jitendra ▴ 10
2
votes
5
replies
680
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 4 months ago by 49k • written 4 months ago by • 0
1
vote
3
replies
435
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 4 months ago by 64k • written 4 months ago by • 0
5
votes
7
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485
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 4 months ago by 49k • written 4 months ago by ▴ 10
1
vote
2
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467
views
loading scores using plotMDS in limma
plotMDS limma
4 months ago Cen • 0
2
votes
1
reply
426
views
Grouping DEGs yields varying results
RNASeq limma
updated 4 months ago by 49k • written 4 months ago by ▴ 10
0
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6
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549
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 4 months ago by 49k • written 4 months ago by • 0
0
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2
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399
views
Fluidigm Data Batch Correction
sva limma
updated 4 months ago by 49k • written 5 months ago by • 0
0
votes
2
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370
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
4 months ago Eleonora • 0
3
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2
replies
336
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 4 months ago by 49k • written 4 months ago by • 0
1
vote
1
reply
503
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 5 months ago by 49k • written 5 months ago by • 0
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4
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416
views
Pairwise comparison for DEG analysis
limma
updated 4 months ago by ★ 3.6k • written 5 months ago by • 0
3
votes
2
replies
651
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 5 months ago by 49k • written 5 months ago by ▴ 10
1
vote
1
reply
331
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 5 months ago by 49k • written 5 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0
This is the result i got when i only looked on day 04 for the gene in example 1 posted above dds_sub <- dds[, dds$date %in% c("day04"…
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE) by James W. MacDonald 64k
There are two types of probes used by Illumina. The type I probes bind directly to the CpG site and have two different probes (one for a me…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by Michael Love 41k
Then for the remaining genes that you don't think are DE, just plot like this: ``` dds_sub <- dds[,dds$condition %in% c("x","y")] dropleve…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0
yes i turned it off @mikelove
Answer: autonomics: example("read_somascan", package = "autonomics") fails, but not on B by Mike Smith ★ 6.2k
It looks like `autonomics` uses `BiocFileCache` to create a local copy of the data and save repeat downloading. Given the (relatively) rec…
Votes
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
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