Showing : Limma • reset
5
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8
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 1 day ago by • 0 • written 7.7 years ago by ▴ 30
6
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5
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6.1k
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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
9
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5
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5.1k
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Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
5
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6
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3.7k
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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
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 22 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
3
votes
11
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2.4k
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Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago • updated 10 months ago Anna ▴ 20
1
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12
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2.4k
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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 2.5 years ago by ▴ 380
4
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8
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2.1k
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Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 16 months ago by ▴ 20
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7
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2.0k
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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
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
15
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22
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1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago Chris • 0
1
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3
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1.8k
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Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
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0
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1.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
1
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6
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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
5
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8
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1.4k
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
0
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2
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1.4k
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Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.6 years ago by ▴ 80
0
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7
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1.4k
views
A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
3
votes
13
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1.3k
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Timely differentially expressed genes
timecoursedata limma
7 months ago • updated 4 months ago triZZla • 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
2
votes
5
replies
1.2k
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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
5
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9
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1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 6 days ago by 50k • written 7 months ago by ▴ 10
0
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5
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1.2k
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[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
3
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2
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1.2k
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Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
3
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3
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1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 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
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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 11 months ago by • 0
2
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3
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1.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
1
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5
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1.0k
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Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
1
reply
957
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
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3
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906
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how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
9 months ago amnahsiddiqa ▴ 10
1
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6
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903
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Limma dispersed distribution of log fold change
limma
written 7 months ago by • 0
0
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4
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893
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Limma multi-group, nested analysis with aggregation
limma
11 months ago • updated 8 months ago Jonathan ▴ 10
0
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5
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888
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
6 months ago dorota.komar • 0
3
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5
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860
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limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 17 months ago by • 0
4
votes
5
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857
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by 50k • written 7 months ago by ▴ 10
5
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9
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849
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 6 days ago Chris • 0
0
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2
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844
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RPPA data (Proteomics analysis)
TCGAbiolinks limma
12 months ago qiz218591 • 0
0
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2
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840
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
11 months ago pg45863 ▴ 10
2
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1
reply
831
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limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 6 months ago by 50k • written 6 months ago by • 0
0
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6
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830
views
Help with model.matrix and creating the right contrast matrix for limma
limma
7 months ago • updated 4 months ago rober204 • 0
3
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6
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825
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
5
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25
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813
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 19 days ago by 50k • written 29 days ago by ▴ 10
1
vote
7
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809
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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5
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802
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Limma continuous design (association polygenic risk score with gene expression)
limma
updated 4 months ago by 50k • written 6 months ago by • 0
1
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3
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784
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
5
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5
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779
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
1
vote
2
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776
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loading scores using plotMDS in limma
plotMDS limma
9 months ago • updated 8 months ago Cen • 0
7
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2
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760
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
0
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6
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757
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
Awards • All
Popular Question to Bine ▴ 40
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
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Scholar to Michael Love 41k
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