Showing : limma • reset
5
votes
8
replies
8.8k
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 14 days ago by • 0 • written 7.7 years ago by ▴ 30
6
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5
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6.2k
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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
replies
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
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
0
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6
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3.1k
views
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
replies
2.7k
views
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
3
votes
11
replies
2.5k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago Anna ▴ 20
1
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12
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2.4k
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 2.5 years ago by ▴ 380
4
votes
8
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2.2k
views
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 17 months ago by ▴ 20
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
15
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23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 6 days ago Chris • 0
11
votes
4
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1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
1
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3
replies
1.8k
views
Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
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0
replies
1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.6 years ago by ▴ 20
0
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3
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1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 6 days ago by • 0 • written 13.0 years ago by ▴ 10
5
votes
8
replies
1.5k
views
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
votes
7
replies
1.4k
views
A question about Limma
PROcess Microarray limma
19.4 years ago • updated 11 months ago Gordon Smyth 50k
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
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata limma
8 months ago • updated 5 months ago triZZla • 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
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 9 months ago by • 0
5
votes
9
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1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 19 days ago by 50k • written 7 months ago by ▴ 10
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
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5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
3
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3
replies
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
14
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17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 5 days ago Chris • 0
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 42k • written 2.9 years ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
2
votes
3
replies
1.1k
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 9 months ago by 65k • written 9 months ago by ▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 6 days ago by • 0 • written 7.9 years ago by • 0
1
vote
5
replies
1.0k
views
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 10 months ago by 50k • written 10 months ago by • 0
1
vote
1
reply
988
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 months ago by 50k • written 10 months ago by • 0
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
3
votes
3
replies
936
views
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
10 months ago amnahsiddiqa ▴ 10
1
vote
6
replies
934
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
5
votes
9
replies
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
votes
5
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927
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
0
votes
4
replies
926
views
Limma multi-group, nested analysis with aggregation
limma
12 months ago • updated 9 months ago Jonathan ▴ 10
3
votes
5
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897
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 18 months ago by • 0
4
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5
replies
875
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by 50k • written 7 months ago by ▴ 10
0
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2
replies
857
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
11 months ago pg45863 ▴ 10
2
votes
1
reply
856
views
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
votes
6
replies
855
views
Help with model.matrix and creating the right contrast matrix for limma
limma
7 months ago • updated 4 months ago rober204 • 0
1
vote
7
replies
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
3
votes
6
replies
844
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
1
vote
2
replies
819
views
loading scores using plotMDS in limma
plotMDS limma
9 months ago Cen • 0
0
votes
5
replies
812
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 5 months ago by 50k • written 6 months ago by • 0
7
votes
2
replies
808
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
5
votes
5
replies
801
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
50 results • Page 1 of 1
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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 42k
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: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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