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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
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
15
votes
17
replies
2.4k
views
Why p value inconsistent when using different number of pathway score?
limma
9 months ago
Chris
▴ 20
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
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
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
7
votes
6
replies
883
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Amit
• 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
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
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
6
votes
5
replies
595
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 5 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
1sunmic2
• 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
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
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
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
4
replies
875
views
Limma with covariates
limma
7 months ago
Chris
▴ 20
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
5
votes
4
replies
556
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 4 months ago by
ATpoint
★ 4.6k • written 4 months ago by
Bioinformagician
• 0
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
4
votes
2
replies
621
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 12 weeks ago by
Gordon Smyth
52k • written 12 weeks ago by
Ahdee
▴ 50
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
4
votes
3
replies
855
views
Analysis of 2*4 factorial design
limma
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Sudipta
• 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
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
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
4
votes
4
replies
693
views
Warning message when running limma with covariates
limma
7 months ago • updated 6 weeks ago
Chris
▴ 20
4
votes
3
replies
658
views
Limma comparing gene expression between base line and one treatment
limma
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
AL
• 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
3
votes
3
replies
650
views
One-sided tests with CAMERA-PR
CAMERA
limma
updated 6 months ago by
Gordon Smyth
52k • written 6 months ago by
Tyler Sagendorf
▴ 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
3
votes
2
replies
848
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 8 months ago by
Gordon Smyth
52k • written 9 months ago by
Kim
• 0
3
votes
3
replies
375
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
4 months ago
Guido Hooiveld
★ 4.1k
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
3
votes
4
replies
715
views
using limma trend workflow in CAMERA
CAMERA
limma
6 months ago • updated 5 months ago
Jay
• 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
3
votes
2
replies
754
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
8 months ago
mohammedtoufiq91
▴ 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
3
votes
4
replies
717
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
3 months ago
dseauer
• 0
3
votes
4
replies
660
views
Help with error using camera() in limma
CAMERA
limma
9 months ago
Chris
▴ 20
3
votes
8
replies
971
views
Constrast for Time Course Experiments using Limma
limma
11 months ago
dl17032000
• 0
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
3
votes
4
replies
893
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
7 months ago
jcollier
• 0
3
votes
3
replies
611
views
voom does not seem to properly correct for library size
limma
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
ATpoint
★ 4.6k
3
votes
3
replies
653
views
Crossover design with limma
limma
crossover
updated 8 weeks ago by
Gordon Smyth
52k • written 10 weeks ago by
Marek Gierlinski
▴ 30
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
2
votes
2
replies
430
views
Automatically generate contrasts from a model matrix / formula
limma
updated 3 months ago by
ATpoint
★ 4.6k • written 4 months ago by
Jonathan
▴ 10
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
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
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
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
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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