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Showing :
Limma
•
reset
3
votes
13
replies
1.2k
views
Timely differentially expressed genes
timecoursedata
limma
6 months ago • updated 4 months ago
triZZla
• 0
1
vote
12
replies
2.2k
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 9 weeks ago by
Mary
• 0 • written 2.4 years ago by
Ming
▴ 380
3
votes
11
replies
1.2k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
alexia.brunel
• 0
3
votes
11
replies
2.2k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
10 months ago • updated 9 months ago
Anna
▴ 20
32
votes
10
replies
37k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 11 months ago by
manuelsokolov
• 0 • written 10.3 years ago by
Jon Bråte
▴ 250
0
votes
9
replies
420
views
limma fo continous variables
limma
DEGseq
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
mia
• 0
0
votes
8
replies
2.0k
views
Limma : time course experiment with missing data
limma
limma-voom
updated 11 months ago by
blackdesgin
• 0 • written 6.0 years ago by
SPbeginner
• 0
1
vote
8
replies
283
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
5
votes
8
replies
1.3k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 3 months ago by
Shaimaa Gamal
• 0 • written 10 months ago by
pg45863
▴ 10
5
votes
8
replies
1.1k
views
Batch correction and repeated measures
RUVSeq
sva
limma
6 months ago • updated 7 days ago
Jonathan
▴ 10
4
votes
8
replies
2.0k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 10 months ago by
Gordon Smyth
50k • written 16 months ago by
Sabiha
▴ 20
3
votes
8
replies
425
views
Constrast for Time Course Experiments using Limma
limma
23 days ago • updated 21 days ago
dl17032000
• 0
0
votes
7
replies
1.3k
views
A question about Limma
PROcess
Microarray
limma
19.2 years ago • updated 10 months ago
Gordon Smyth
50k
4
votes
7
replies
2.0k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 8 months ago by
Gordon Smyth
50k • written 7.8 years ago by
nathan
• 0
1
vote
7
replies
744
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 5 months ago by
Gimena
• 0
4
votes
7
replies
331
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
5
votes
7
replies
697
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Jonathan
▴ 10
8
votes
6
replies
341
views
DGE analysis with LIMMA
limma
updated 27 days ago by
Gordon Smyth
50k • written 27 days ago by
Amit
• 0
7
votes
6
replies
333
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
2
votes
6
replies
2.4k
views
RNA-seq analysis across different experiments
limma
deseq2
normalization
degenes
design and contrast matrix
written 6.7 years ago by
mrigaya.mehra
▴ 10
5
votes
6
replies
3.6k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 9 weeks ago by
briankleiboeker
• 0 • written 3.0 years ago by
r.i.s.alnuwaysir
▴ 10
1
vote
6
replies
1.6k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 7 months ago by
Gordon Smyth
50k • written 3.5 years ago by
linouhao
▴ 20
4
votes
6
replies
495
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 7 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Shaimaa Gamal
• 0
0
votes
6
replies
778
views
Help with model.matrix and creating the right contrast matrix for limma
limma
6 months ago • updated 3 months ago
rober204
• 0
0
votes
6
replies
718
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gld-bioinf
• 0
0
votes
6
replies
325
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 days ago • updated 3 days ago
Lily Cheang
• 0
3
votes
6
replies
779
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
1
vote
6
replies
845
views
Limma dispersed distribution of log fold change
limma
written 7 months ago by
Erin Yu
• 0
1
vote
6
replies
2.6k
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 7.4 years ago by
Camila Orellana
▴ 10
3
votes
5
replies
805
views
limma-trend vs. limma-voom theoretical difference
limma
limma-trend
limma-voom
updated 10 weeks ago by
floriandeckert
▴ 30 • written 16 months ago by
hainct
• 0
3
votes
5
replies
545
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 25 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 4 months ago by
Gordon Smyth
50k • written 8.1 years ago by
Radek
▴ 90
2
votes
5
replies
1.1k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Sara
• 0
0
votes
5
replies
1.1k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 12 months ago by
andrewsm
• 0
0
votes
5
replies
757
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
e.vanzanten.1
• 0
4
votes
5
replies
826
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
5
votes
5
replies
727
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
7 months ago
Jitendra
▴ 10
6
votes
5
replies
5.8k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 6 months ago by
Gordon Smyth
50k • written 2.4 years ago by
David Lyon
▴ 340
1
vote
5
replies
945
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 8 months ago by
Gordon Smyth
50k • written 9 months ago by
manuelsokolov
• 0
0
votes
5
replies
450
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 11 weeks ago by
ATpoint
★ 4.0k • written 12 weeks ago by
Xiao
• 0
0
votes
5
replies
821
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
5 months ago
dorota.komar
• 0
0
votes
5
replies
129
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Jitendra
▴ 10
3
votes
4
replies
678
views
Anova table edgeR limma
limma
RNASeq
edgeR
10 months ago
KATHERINE CHUERE NUNES
• 0
2
votes
4
replies
536
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
kyj2226
• 0
1
vote
4
replies
553
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
0
votes
4
replies
1.2k
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics
limma
MassSpectrometry
updated 11 months ago by
Gordon Smyth
50k • written 2.8 years ago by
barrypraveen
• 0
0
votes
4
replies
276
views
limma with interaction term
R
biostatistics
limma
Epigenetics
6 weeks ago • updated 4 weeks ago
Jitendra
▴ 10
1
vote
4
replies
678
views
Pairwise differential expression using limma
limma
9 months ago • updated 8 months ago
Melissa
• 0
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 6 months ago by
Gordon Smyth
50k • written 5.1 years ago by
tleona3
• 0
1
vote
4
replies
292
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
50 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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