Showing : LIMMA • reset
0
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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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542
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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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331
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 2 days ago by 50k • written 2 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
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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
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11
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1.3k
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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
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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
8
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6
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460
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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
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Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 5 days ago Chris • 0
1
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6
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930
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
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7
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844
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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
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3
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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
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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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619
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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
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352
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 21 days ago by 50k • written 26 days ago by • 0
1
vote
3
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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
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4
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373
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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
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2
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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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924
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
votes
4
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635
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
0
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2
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322
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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
101
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Gene-by-sample covariates in limma
Metabolomics limma
updated 3 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
10 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 5 weeks ago by ▴ 10
5
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2
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690
views
PhD student
TMM limma
10 months ago Nisha • 0
1
vote
1
reply
365
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
5
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5
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800
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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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610
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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
25 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
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265
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
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…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset) by Caio • 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Votes
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
Answer: Help with running egsea()
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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