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 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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534
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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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306
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 1 day ago by 50k • written 1 day 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
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A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
1
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3
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404
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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
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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557
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
8
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6
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456
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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 4 days ago by • 0 • written 13.0 years ago by ▴ 10
1
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2
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466
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Assess fit of variance prior
limma
updated 4 months ago by 50k • written 4 months ago by ▴ 20
3
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2
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448
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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
14 days ago • updated 3 days ago Chris • 0
1
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6
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927
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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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837
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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 6 months ago by • 0
0
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3
replies
458
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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
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5
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1.3k
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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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618
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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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347
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 24 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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369
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limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 9 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
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5
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921
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
452
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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630
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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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317
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Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 9 weeks ago alessandro • 0
0
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1
reply
84
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Gene-by-sample covariates in limma
Metabolomics limma
updated 2 days ago by 50k • written 2 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 11 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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1
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498
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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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292
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limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
3
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1
reply
173
views
Log-cpm values from limma
limma edgeR RNASeq
updated 15 days ago by 50k • written 16 days 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 3.1 years ago by ▴ 10
2
votes
1
reply
301
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
726
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Pairwise differential expression using limma
limma
10 months ago Melissa • 0
4
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7
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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
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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
923
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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689
views
PhD student
TMM limma
10 months ago Nisha • 0
1
vote
1
reply
363
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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796
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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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606
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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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921
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Light difference when using coef vs omit a group when compare 3 groups.
limma
24 days ago • updated 16 days ago Chris • 0
0
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9
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560
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limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
2
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3
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367
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
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2
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258
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
12 weeks ago Lily Cheang ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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