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Showing :
Limma
•
reset
18
votes
37
replies
16k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
8.9 years ago • updated 8.7 years ago
svlachavas
▴ 830
2
votes
30
replies
4.0k
views
create design matrix when 2 groups of gene-expression data
limma
8.3 years ago • updated 8.0 years ago
mheydarpour
▴ 10
2
votes
25
replies
6.1k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
8.0 years ago • updated 7.9 years ago
sami.pietila
• 0
6
votes
25
replies
3.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 8.1 years ago by
cstrato
★ 3.9k • written 8.1 years ago by
Biologist
▴ 110
5
votes
25
replies
778
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 24 days ago by
Jitendra
▴ 10
9
votes
21
replies
5.3k
views
limma - complex design with paired samples, sex and batch effect
limma
paired samples
complex-design
8.3 years ago
aec
▴ 90
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.6 years ago
osa.zuta
▴ 40
9
votes
21
replies
3.3k
views
Error when fitting linear model with technical replicates and blocking variable
limma
technical replicates
8.4 years ago
Eleni Christodoulou
▴ 150
12
votes
20
replies
2.0k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma
multifactorial design
design and contrast matrix
affymetrix microarrays
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
svlachavas
▴ 830
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 11 days ago
Chris
• 0
3
votes
19
replies
3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.1 years ago
mheydarpour
▴ 10
7
votes
18
replies
8.3k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.6 years ago
Radek
▴ 90
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma
batch effect
ComBat
differential gene expression
updated 8.5 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
svlachavas
▴ 830
1
vote
18
replies
2.0k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma
design matrix
matrix with covariables
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
michel655
• 0
11
votes
18
replies
4.8k
views
What is the correct use of removeBatchEffect's design parameter
deseq2
limma
updated 3.1 years ago by
Gordon Smyth
50k • written 3.6 years ago by
Sam
▴ 10
5
votes
18
replies
1.7k
views
Difference of difference, paired design
edger
deseq2
limma
updated 4.8 years ago by
swbarnes2
★ 1.3k • written 4.8 years ago by
Bloodgas
• 0
3
votes
17
replies
4.3k
views
filtering probes in affymetrix data
Annotation
limma
Annotation
limma
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Sabet, Julia A
▴ 180
0
votes
17
replies
1.6k
views
How to check linear model
modalmatrix
limma
R
linear
14 months ago • updated 13 months ago
Jitendra
▴ 10
4
votes
17
replies
2.6k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma
r
differential gene expression
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
Biologist
▴ 110
0
votes
17
replies
2.3k
views
Testing for no change in RNA-seq data?
limma
limma
updated 11.1 years ago by
Simon Anders
★ 3.7k • written 11.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
17
replies
2.2k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 14 months ago by
Gordon Smyth
50k • written 18 months ago by
Sam
• 0
3
votes
16
replies
4.1k
views
limma contrast matrix
limma
contrast
design and contrast matrix
9.4 years ago
Smith H.
▴ 20
7
votes
16
replies
4.3k
views
limma voom and trend
limma
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
linouhao
▴ 20
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma
differential gene expression
microarray
linear model
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
bcbio_uk
▴ 10
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
7.9 years ago
giroudpaul
▴ 40
4
votes
16
replies
4.5k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
joseale2310
▴ 10
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma
multifactorial design
diagnostic plots
affymetrix microarrays
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
svlachavas
▴ 830
3
votes
15
replies
2.7k
views
Are the p-values supposed to be on the order of 10^-120?
limma
affy
bioconductor
affymetrix
updated 9.5 years ago by
Gordon Smyth
50k • written 9.5 years ago by
mccallionc403
• 0
8
votes
15
replies
8.6k
views
Design matrix for continuous independent variable in limma
limma
microarray
8.3 years ago
Linda Chaba
▴ 10
2
votes
15
replies
3.0k
views
limma: how to use pairing and adjust for covariates
limma
limma-voom
limma paired analysis
limma contrast matrix
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
gregory.l.stone
▴ 10
0
votes
15
replies
2.2k
views
Exon array annotation with limma?
Normalization
limma
biomaRt
oneChannelGUI
Normalization
limma
biomaRt
oneChannelGUI
updated 14.3 years ago by
rcaloger
▴ 500 • written 14.3 years ago by
Michael Imbeault
▴ 220
0
votes
15
replies
2.6k
views
PreFiltering probe in microarray analysis
Microarray
limma
oligo
Microarray
limma
oligo
updated 12.9 years ago by
wxu@msi.umn.edu
▴ 220 • written 12.9 years ago by
Stephanie PIERSON
▴ 30
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
9.4 years ago • updated 9.3 years ago
vas
▴ 40
10
votes
14
replies
4.2k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Nik Tuzov
▴ 80
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma
microarray
updated 9.2 years ago by
Sean Davis
21k • written 9.2 years ago by
Andreas Heider
▴ 340
2
votes
14
replies
3.5k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma
oligo
annotation
updated 9.1 years ago by
alakatos
▴ 130 • written 9.3 years ago by
aminbau14
• 0
6
votes
14
replies
2.9k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA
FireBrowse
limma
DEG
updated 6.0 years ago by
svlachavas
▴ 830 • written 6.0 years ago by
lawarde.ankita1
▴ 30
6
votes
14
replies
3.0k
views
limma with continous covariate depending on gene, 2 block variables, pairing and technical replicates
limma
covariate
block
paired samples
technical replicates
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
eleonoregravier
▴ 70
6
votes
14
replies
2.1k
views
Help analyzing RNA-seq data from FPKM values with multiple time points
rnaseq
limma
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
rsrzkk
• 0
0
votes
14
replies
2.2k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe
limma
ArrayExpress
probe
limma
ArrayExpress
updated 13.0 years ago by
Wei Shi
★ 3.6k • written 13.0 years ago by
Gavin Koh
▴ 220
8
votes
14
replies
2.8k
views
Batch with only one sample or condition
limma
batch effect
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
eleonoregravier
▴ 70
17
votes
14
replies
39k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 22 months ago by
OE
• 0 • written 6.7 years ago by
cms72
▴ 20
16
votes
13
replies
4.3k
views
Camera and ROAST
limma
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Nuno Pires
▴ 30
2
votes
13
replies
2.1k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom
design matrix
limma time-course
limma design matrix
limma
6.1 years ago
SPbeginner
• 0
2
votes
13
replies
1.9k
views
problem about (design matrix)
limma
limma design matrix
design matrix
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
libya.tahani
• 0
0
votes
13
replies
2.4k
views
two color arrays normalization
limma
limma
updated 15.2 years ago by
Jenny Drnevich
★ 2.0k • written 15.2 years ago by
Giusy Della Gatta
▴ 110
0
votes
13
replies
2.7k
views
LIMMA decideTests result zero from contrast matrix
limma
limma
12.0 years ago
Ekta Jain
▴ 370
7
votes
13
replies
1.8k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma
microarray
hugeneST
batch effect
DE
updated 5.2 years ago by
Ryan C. Thompson
★ 7.9k • written 5.2 years ago by
svlachavas
▴ 830
1
vote
13
replies
2.3k
views
Why Differential expression results differ with edgeR and limma ?
limma
edgeR
differential gene expression
r
6.7 years ago
Biologist
▴ 110
0
votes
13
replies
2.4k
views
handling missing data (NA) for methylaion analysis in Limma
limma
missing data
methylation
normalization
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mheydarpour
▴ 10
50 results • Page
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Replies
Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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