Showing : limma • reset
0
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3.1k
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limma, analysis on subset of data gives completely different results
limma limma
updated 4 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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543
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
1
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2
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334
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 3 days ago by 50k • written 3 days ago by • 0
11
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4
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1.8k
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LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
0
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7
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1.4k
views
A question about Limma
PROcess Microarray limma
19.4 years ago • updated 11 months ago Gordon Smyth 50k
1
vote
3
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410
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
5
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2
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561
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
8
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6
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462
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DGE analysis with LIMMA
limma
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 6 days ago by • 0 • written 13.0 years ago by ▴ 10
1
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2
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467
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Assess fit of variance prior
limma
updated 4 months ago by 50k • written 5 months ago by ▴ 20
3
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2
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451
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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
14
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17
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1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 5 days ago Chris • 0
1
vote
6
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933
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
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
7
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845
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
0
votes
3
replies
460
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
2
votes
5
replies
1.3k
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
0
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2
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621
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Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
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3
replies
352
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 21 days ago by 50k • written 27 days ago by • 0
1
vote
3
replies
1.8k
views
Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
6
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5
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6.2k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
0
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4
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374
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limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 10 weeks ago Jitendra ▴ 10
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
4
votes
2
replies
1.2k
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
5
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926
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
7
votes
6
replies
459
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
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4
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638
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
0
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2
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323
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Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 10 weeks ago alessandro • 0
0
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1
reply
103
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Gene-by-sample covariates in limma
Metabolomics limma
updated 4 days ago by 50k • written 4 days ago by • 0
5
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8
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8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 13 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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1
reply
500
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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 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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2
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297
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limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 17 days ago by 50k • written 18 days ago by • 0
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
2
votes
1
reply
305
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
1
vote
4
replies
727
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
4
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7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 7.9 years ago by • 0
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
5
votes
25
replies
938
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 4 weeks ago by 50k • written 6 weeks ago by ▴ 10
5
votes
2
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690
views
PhD student
TMM limma
10 months ago Nisha • 0
1
vote
1
reply
366
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
5
votes
5
replies
801
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
2
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4
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611
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
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3
replies
418
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 4 months ago by ▴ 350 • written 4 months ago by • 0
5
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9
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930
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
26 days ago • updated 18 days ago Chris • 0
0
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9
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564
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limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
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3
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372
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
0
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2
replies
267
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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