Showing : limma • reset
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3.1k
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limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
1
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6
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2.7k
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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 7.5 years ago by ▴ 10
2
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8
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564
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
3
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2
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465
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For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
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11
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1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 11 months ago by • 0
15
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17
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1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
29 days ago • updated 17 days ago Chris ▴ 10
5
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2
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602
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
0
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4
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394
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
0
votes
2
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650
views
Fluidigm Data Batch Correction
sva limma
updated 10 months ago by 50k • written 10 months ago by • 0
8
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6
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505
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DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
1
vote
2
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473
views
Assess fit of variance prior
limma
updated 5 months ago by 50k • written 5 months ago by ▴ 20
9
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5
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5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
1
vote
6
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953
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
1
vote
2
replies
405
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 15 days ago by 50k • written 15 days ago by • 0
1
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3
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1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
7
replies
879
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
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3
replies
481
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.3 years ago by • 0
1
vote
3
replies
369
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
0
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3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 18 days ago by • 0 • written 13.1 years ago by ▴ 10
6
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5
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6.3k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
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5
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971
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
7 months ago dorota.komar • 0
1
vote
3
replies
440
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
1
reply
158
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 16 days ago by 50k • written 16 days ago by • 0
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
0
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2
replies
322
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
5
votes
3
replies
312
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Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 4 weeks ago by • 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 26 days ago by • 0 • written 7.8 years ago by ▴ 30
1
vote
3
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666
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 9 months ago by 50k • written 9 months ago by • 0
2
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1
reply
313
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 5 months ago by 50k • written 5 months ago by • 0
5
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6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 10
0
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1
reply
56
views
Subsetting RNAseq data | voomaByGroup()
limma
updated 2 hours ago by 50k • written 1 day ago by • 0
0
votes
3
replies
429
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 5 months ago by ▴ 350 • written 5 months ago by • 0
1
vote
1
reply
373
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
1.4k
views
Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.7 years ago by ▴ 80
0
votes
1
reply
512
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
5
votes
5
replies
826
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
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2
replies
301
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
5
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9
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976
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Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
0
votes
6
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810
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 10 months ago by • 0
1
vote
2
replies
615
views
Extracting fitted expression matrix from Limma
limma
11 months ago sarah.kelliher • 0
5
votes
2
replies
701
views
PhD student
TMM limma
10 months ago Nisha • 0
0
votes
6
replies
868
views
Help with model.matrix and creating the right contrast matrix for limma
limma
8 months ago • updated 5 months ago rober204 • 0
1
vote
4
replies
747
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
0
votes
9
replies
592
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
1
vote
12
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2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 3 months ago by • 0 • written 2.6 years ago by ▴ 380
50 results • Page 1 of 1
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Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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