Showing : Limma • reset
0
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6
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3.1k
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limma, analysis on subset of data gives completely different results
limma limma
updated 17 days ago by 50k • written 9.8 years ago by ▴ 40
1
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6
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2.6k
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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 7.4 years ago by ▴ 10
2
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8
replies
473
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 22 days ago by 50k • written 24 days ago by • 0
0
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7
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1.4k
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A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
6
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5
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6.0k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
1
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3
replies
1.7k
views
Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 days ago by 50k • written 9 days ago by • 0
0
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5
replies
871
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
6 months ago dorota.komar • 0
8
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6
replies
418
views
DGE analysis with LIMMA
limma
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
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325
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limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 7 weeks ago Jitendra ▴ 10
0
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3
replies
352
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
11
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4
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1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 6 months ago by 50k • written 5.2 years ago by • 0
9
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5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
1
vote
6
replies
887
views
Limma dispersed distribution of log fold change
limma
written 7 months ago by • 0
3
votes
2
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1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
1
vote
2
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448
views
Assess fit of variance prior
limma
updated 4 months ago by 50k • written 4 months ago by ▴ 20
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 9 months ago by 50k • written 10 months ago by • 0
2
votes
5
replies
1.2k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
3
votes
2
replies
426
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 months ago by 50k • written 9 months ago by • 0
5
votes
2
replies
510
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
2
replies
595
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
3
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431
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
1
vote
7
replies
798
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
0
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2
replies
583
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
3
votes
5
replies
847
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 17 months ago by • 0
0
votes
1
reply
205
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 28 days ago by 50k • written 28 days ago by • 0
7
votes
6
replies
410
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 27 days ago by 50k • written 27 days ago by • 0
2
votes
4
replies
595
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
3
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11
replies
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
10 months ago Anna ▴ 20
0
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2
replies
264
views
limma model matrix questions
limmaGUI limma pairedsamples
8 weeks ago whyw6948 • 0
1
vote
3
replies
613
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 8 months ago by 50k • written 8 months ago by • 0
2
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4
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1.1k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 7 months ago by 41k • written 2.9 years ago by • 0
1
vote
6
replies
1.7k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
1
vote
3
replies
775
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
1
reply
59
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 hours ago by 50k • written 1 day ago by • 0
2
votes
1
reply
280
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
2
replies
292
views
Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 7 weeks ago alessandro • 0
5
votes
2
replies
665
views
PhD student
TMM limma
9 months ago Nisha • 0
5
votes
5
replies
770
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
1
vote
1
reply
335
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
2
votes
4
replies
581
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
votes
3
replies
390
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 4 months ago by ▴ 350 • written 4 months ago by • 0
1
vote
4
replies
701
views
Pairwise differential expression using limma
limma
9 months ago Melissa • 0
0
votes
9
replies
507
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limma fo continous variables
limma DEGseq
updated 7 weeks ago by 65k • written 8 weeks ago by • 0
2
votes
3
replies
333
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
2
replies
236
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
10 weeks ago Lily Cheang ▴ 10
0
votes
1
reply
487
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 7 months ago by ★ 4.0k • written 7 months ago by • 0
5
votes
25
replies
784
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 14 days ago by 50k • written 24 days ago by ▴ 10
4
votes
7
replies
2.0k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 8 months ago by 50k • written 7.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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