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LIMMA
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0
votes
1
reply
2.6k
views
bigwig to counts
DESeq2
edgeR
bigwig
limma
3.3 years ago • updated 3.0 years ago
Bogdan
▴ 670
1
vote
1
reply
1.4k
views
Weird distribution of p-values, with no significant adjusted p-values?
fdr
limmaGUI
p-values
limma
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
seahorsebox828
• 0
0
votes
7
replies
2.2k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma
Paireddata
DifferentialExpression
updated 3.2 years ago by
James W. MacDonald
68k • written 3.3 years ago by
r02eb20
• 0
1
vote
2
replies
1.8k
views
Limma adj.p.value the same for many different p.values
limmaGUI
limma
adj.p.value
StatisticalMethod
3.3 years ago
walkerrh95
• 0
3
votes
7
replies
3.1k
views
Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2
limma
updated 3.3 years ago by
swbarnes2
★ 1.4k • written 3.3 years ago by
Bine
▴ 50
5
votes
8
replies
3.1k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
3.3 years ago • updated 3.1 years ago
mohammedtoufiq91
▴ 10
0
votes
11
replies
2.4k
views
limma::contrast.fit() potential bugs when weights from voom() included
bugs
limma
3.4 years ago
Zhenyu
• 0
2
votes
3
replies
1.3k
views
limma::goana - "Invalid value for odds"
limma
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
neilzhao
▴ 30
0
votes
0
replies
959
views
Finding DEGs between two different datasets using limma
Proteomics
limma
proteomi
3.4 years ago
mfaleevs
• 0
5
votes
6
replies
2.7k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
Kent
• 0
0
votes
0
replies
835
views
Tuning the MetaVolcanoR plots
limma
MetaVolcanoR
3.4 years ago
JAcky
• 0
1
vote
10
replies
4.3k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma
voom
3.4 years ago
Hilary
▴ 40
0
votes
3
replies
1.6k
views
Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates not of…
limma
Proteomics
ProteomicsWorkflow
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
samantha.v.goncalves
• 0
2
votes
2
replies
1.2k
views
paired samples, comparing expression given a continuous variable
limma
updated 3.4 years ago by
Gordon Smyth
53k • written 3.5 years ago by
naz
• 0
1
vote
1
reply
934
views
ordinal treatment group design / contrast matrix
limma
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Chris
• 0
0
votes
1
reply
1.5k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
mfaleevs
• 0
1
vote
1
reply
964
views
IS DGE possible with normalized microarray expression data and Limma ?
limma
MicroarrayData
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
waltheja
• 0
2
votes
2
replies
2.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
3.5 years ago
Yang Shi
▴ 10
2
votes
4
replies
2.2k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
Yang Shi
▴ 10
5
votes
6
replies
2.8k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
3.5 years ago
Yang Shi
▴ 10
2
votes
4
replies
2.8k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
3.5 years ago
Yang Shi
▴ 10
0
votes
0
replies
1000
views
MetaVolcanoR usage
limma
MetaVolcanoR
EnhancedVolcano
3.5 years ago
JAcky
• 0
3
votes
4
replies
1.6k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma
RNASeq
Expected_count
DESeq2
3.5 years ago
Yang Shi
▴ 10
1
vote
1
reply
1.1k
views
Weight Array Quality before of after applying variance filtering?
limma
arrays
genefilter
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
jacorvar
▴ 40
2
votes
6
replies
2.1k
views
Limma beta coefficient confidence intervals
limma
limmaGUI
beta
3.6 years ago
fluentin44
• 0
0
votes
1
reply
1.3k
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
Sam
• 0
3
votes
9
replies
3.1k
views
Help with limma contrast, difference of a difference?
limma
3.6 years ago
Ahdee
▴ 60
0
votes
8
replies
2.3k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
3.6 years ago
YC
• 0
0
votes
3
replies
3.3k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 3.6 years ago by
shepherl
4.3k • written 3.6 years ago by
Jenny Drnevich
★ 2.0k
0
votes
2
replies
1.1k
views
Get confused about the mean log-intensity (Amean)
limma
3.6 years ago
OE
• 0
2
votes
9
replies
4.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
3.6 years ago
Peipei
• 0
1
vote
8
replies
2.4k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression
celltype
treatment
edgeR
limma
3.6 years ago
giBio
• 0
0
votes
2
replies
1.6k
views
How do I remove the outlier probes highlighted in the plotSA function of limma
limma
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
S
• 0
1
vote
2
replies
1.4k
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
3.6 years ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
2.0k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
3.6 years ago
Mikołaj Mierzejewski
• 0
2
votes
1
reply
2.2k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
nhaus
▴ 70
6
votes
2
replies
3.6k
views
Pseudo-bulk Limma Approaches
limma
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
andrew.j.skelton73
▴ 370
9
votes
3
replies
10k
views
Limma vs deseq2 results
limma
RNASeq
R
3.7 years ago • updated 3.6 years ago
k___
▴ 30
2
votes
2
replies
1.4k
views
Help with constructing design matrix for edgeR/limma
limma
design.matrix
model.matrix
edgeR
3.7 years ago • updated 3.6 years ago
adrianna_07
• 0
1
vote
4
replies
1.6k
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
beslinail
• 0
1
vote
1
reply
1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 3.7 years ago by
ATpoint
★ 5.0k • written 3.7 years ago by
Dimitris
• 0
3
votes
3
replies
2.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
mohammedtoufiq91
▴ 10
0
votes
6
replies
2.1k
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
3.7 years ago
Jitendra
▴ 10
0
votes
2
replies
1.8k
views
Using limma to read Illumina HT-12 v4 data
limma
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
orbitofrontal
• 0
4
votes
6
replies
2.5k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
3.7 years ago
mohammedtoufiq91
▴ 10
3
votes
4
replies
2.9k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
3.7 years ago
Yang Shi
▴ 10
2
votes
2
replies
2.8k
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
dr
▴ 10
1
vote
2
replies
1.5k
views
toptable sort .by set
limma
rnaseqGene
3.7 years ago
snowmattin
• 0
1
vote
5
replies
3.3k
views
Unsuccessful DE analysis using limma - voom
limma
3.7 years ago
JAcky
• 0
2
votes
1
reply
1.7k
views
Extremely low P-values when using Limma on high sample size proteomics data
limma
Proteomics
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
roger.moreno.justicia
• 0
4,230 results • Page
7 of 85
Recent ...
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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