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Showing :
Limma
•
reset
34
votes
11
replies
42k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.2 years ago by
Jon Bråte
▴ 260
5
votes
8
replies
9.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 9 months ago by
hortense96
• 0 • written 8.5 years ago by
dmcleanuk
▴ 30
17
votes
9
replies
7.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 4 months ago by
James W. MacDonald
68k • written 8.7 years ago by
ompandey
▴ 10
8
votes
3
replies
4.3k
views
Appropriate ways to filter counts data for voom/limma
limma
edger
sequencing
written 8.5 years ago by
blofeld
▴ 10
15
votes
23
replies
3.6k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
10 months ago • updated 9 months ago
Chris
▴ 20
0
votes
6
replies
3.5k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 10 months ago by
Gordon Smyth
52k • written 10.6 years ago by
Arvid Sondén
▴ 40
6
votes
10
replies
2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 9 weeks ago by
ATpoint
★ 4.6k • written 10 weeks ago by
mohammedtoufiq91
▴ 10
2
votes
6
replies
2.5k
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
10 months ago
Chris
▴ 20
15
votes
17
replies
2.4k
views
Why p value inconsistent when using different number of pathway score?
limma
9 months ago
Chris
▴ 20
6
votes
6
replies
2.4k
views
limma plotMDS - logFC inverted?
limma
MultidimensionalScaling
updated 5 months ago by
James W. MacDonald
68k • written 2.2 years ago by
Katharina
• 0
7
votes
3
replies
2.2k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
written 14 months ago by
annikagable
• 0
5
votes
9
replies
2.1k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 10 months ago by
Gordon Smyth
52k • written 16 months ago by
Jonathan
▴ 10
3
votes
2
replies
2.0k
views
Multi-level design RRBS analysis with voomLmFit
edgeR
voomLmFit
limma
duplicateCorrelation
voom
updated 3 months ago by
Gordon Smyth
52k • written 3.2 years ago by
altintas.ali
• 0
5
votes
25
replies
1.9k
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Jitendra
▴ 10
3
votes
1
reply
1.9k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 9 months ago by
Gordon Smyth
52k • written 6.3 years ago by
CantExitVIM
▴ 10
4
votes
14
replies
1.8k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 6 months ago by
Gordon Smyth
52k • written 7 months ago by
Michael E
• 0
2
votes
12
replies
1.8k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
3 months ago • updated 11 weeks ago
john
• 0
0
votes
2
replies
1.8k
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
11 months ago
kcarey
• 0
0
votes
3
replies
1.8k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 9 months ago by
XW
• 0 • written 13.8 years ago by
Babara Mueller
▴ 10
0
votes
3
replies
1.6k
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP
limma
Bioconductor
ChAMPdata
updated 2 days ago by
81becky
• 0 • written 3.5 years ago by
Jinyue
• 0
0
votes
8
replies
1.6k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix
limma
7 months ago
jiachengd
• 0
2
votes
5
replies
1.6k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq
limma
edgeR
updated 5 months ago by
Sara
• 0 • written 4.3 years ago by
zliu
▴ 10
5
votes
9
replies
1.6k
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
10 months ago
Chris
▴ 20
0
votes
7
replies
1.6k
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
10 months ago • updated 9 months ago
hortense96
• 0
4
votes
6
replies
1.6k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
abadgerw
• 0
0
votes
9
replies
1.6k
views
limma fo continous variables
limma
DEGseq
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
mia
• 0
2
votes
1
reply
1.6k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
danphillips28
▴ 10
3
votes
13
replies
1.4k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq
limma
updated 8 months ago by
Masongeorge
• 0 • written 8 months ago by
ij283
• 0
1
vote
1
reply
1.4k
views
A question about paired data and how to set up the designmatrix in LIMMA
limma
affydata
19.6 years ago • updated 7 months ago
Gordon Smyth
52k
1
vote
8
replies
1.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 3 months ago by
Adam Marstrand
• 0
4
votes
4
replies
1.3k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
7 months ago
sukeshinik5
▴ 20
2
votes
3
replies
1.3k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 9 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
giulia.gentile
▴ 10
2
votes
2
replies
1.3k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 9 months ago by
XW
• 0 • written 8.7 years ago by
tati6406
• 0
3
votes
5
replies
1.2k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 11 months ago by
Michael Love
43k • written 11 months ago by
sap275
▴ 10
4
votes
6
replies
1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
3 months ago
altintas.ali
• 0
3
votes
10
replies
1.2k
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Abbey
• 0
2
votes
6
replies
1.1k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
11 months ago • updated 10 months ago
Lily Cheang
▴ 10
5
votes
7
replies
1.1k
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 10 months ago by
Gordon Smyth
52k • written 11 months ago by
Amit
• 0
5
votes
3
replies
1.1k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 months ago by
Gordon Smyth
52k • written 10 months ago by
Shaimaa Gamal
• 0
0
votes
4
replies
1.1k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 10 months ago by
Michael Love
43k • written 15 months ago by
Crystal571
• 0
1
vote
2
replies
1.0k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
3 months ago
Ai
• 0
3
votes
3
replies
995
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 3 months ago by
Satoshi
• 0
2
votes
8
replies
992
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Amit
• 0
0
votes
9
replies
989
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 9 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
abadgerw
• 0
3
votes
8
replies
971
views
Constrast for Time Course Experiments using Limma
limma
11 months ago
dl17032000
• 0
8
votes
6
replies
957
views
DGE analysis with LIMMA
limma
updated 11 months ago by
Gordon Smyth
52k • written 11 months ago by
Amit
• 0
2
votes
3
replies
942
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 12 weeks ago by
Gordon Smyth
52k • written 3 months ago by
kyj2226
• 0
0
votes
1
reply
923
views
Unable to install/use limma
limma
Bioconductor
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
Jennifer
• 0
1
vote
5
replies
914
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
Xuan Yi
• 0
3
votes
4
replies
892
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
7 months ago
jcollier
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell
by
James W. MacDonald
68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20
by
James W. MacDonald
68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2
by
caroline.zanchi
• 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org
by
Sean Davis
21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
A: Rtracklayer fails to export TxDb as GFF3 without CDS
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