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Showing :
limma
•
reset
1
vote
9
replies
1.8k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 14 months ago by
anna.cot.anna.cot
▴ 40
0
votes
2
replies
851
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
14 months ago
Tadeoye
▴ 20
0
votes
2
replies
1.1k
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
Lina
▴ 10
2
votes
3
replies
2.0k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
giulia.gentile
▴ 10
1
vote
2
replies
781
views
contrast matrix design for a continuous variable
limma
15 months ago • updated 13 months ago
dtzhu337
• 0
3
votes
3
replies
1.1k
views
Crossover design with limma
limma
crossover
updated 14 months ago by
Gordon Smyth
53k • written 15 months ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
2.0k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
abadgerw
• 0
6
votes
10
replies
3.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 14 months ago by
ATpoint
★ 5.0k • written 15 months ago by
mohammedtoufiq91
▴ 10
1
vote
3
replies
882
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 15 months ago by
Melisa Tecik
• 0
0
votes
2
replies
453
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
15 months ago
giulia.gentile
▴ 10
4
votes
2
replies
1.7k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
Ahdee
▴ 60
1
vote
2
replies
561
views
Limma Interaction Effect with Covariates
limma
DMRcate
15 months ago
kitzhu
• 0
2
votes
3
replies
1.6k
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
kyj2226
• 0
3
votes
4
replies
1.3k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
15 months ago
dseauer
• 0
1
vote
3
replies
1.1k
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
15 months ago
abadgerw
• 0
0
votes
5
replies
1.3k
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
15 months ago
abadgerw
• 0
1
vote
8
replies
3.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 16 months ago by
Adam Marstrand
• 0
1
vote
2
replies
1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
16 months ago
Ai
• 0
3
votes
3
replies
1.8k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 16 months ago by
Satoshi
• 0
4
votes
3
replies
1.3k
views
Analysis of 2*4 factorial design
limma
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Sudipta
• 0
2
votes
12
replies
3.0k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
16 months ago • updated 15 months ago
john
• 0
4
votes
6
replies
2.0k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
abadgerw
• 0
4
votes
6
replies
2.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
16 months ago
altintas.ali
• 0
2
votes
2
replies
1.3k
views
Automatically generate contrasts from a model matrix / formula
limma
updated 16 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Jonathan
▴ 10
3
votes
3
replies
879
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
16 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
844
views
Need help interpreting heatmaps from limma
limma
written 16 months ago by
lhwh1208
• 0
2
votes
1
reply
2.0k
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 16 months ago by
James W. MacDonald
68k • written 16 months ago by
danphillips28
▴ 10
5
votes
4
replies
1.2k
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
Bioinformagician
• 0
1
vote
2
replies
1.0k
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Ben
▴ 10
0
votes
0
replies
548
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
17 months ago
tim.meese
• 0
0
votes
2
replies
931
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
blmurphy
• 0
0
votes
2
replies
770
views
Question on performing ANOVA-like analysis using limma
limma
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
grubble
• 0
17
votes
9
replies
8.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 17 months ago by
James W. MacDonald
68k • written 9.8 years ago by
ompandey
▴ 10
2
votes
1
reply
957
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
rae.alshammari
▴ 20
0
votes
1
reply
2.7k
views
Unable to install/use limma
limma
Bioconductor
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Jennifer
• 0
3
votes
3
replies
1.1k
views
voom does not seem to properly correct for library size
limma
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
ATpoint
★ 5.0k
1
vote
5
replies
1.9k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Xuan Yi
• 0
0
votes
3
replies
1.1k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2
limma
DifferentialExpression
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Jiahao Tian
• 0
4
votes
6
replies
1.7k
views
using limma trend workflow in CAMERA
CAMERA
limma
updated 25 days ago by
Gordon Smyth
53k • written 18 months ago by
Jiahao Tian
• 0
3
votes
3
replies
1.1k
views
One-sided tests with CAMERA-PR
CAMERA
limma
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Tyler Sagendorf
▴ 10
1
vote
6
replies
1.5k
views
limma and Syntactically Invalid Factor Values
limma
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
1.2k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
19 months ago
Bioinformagician
• 0
5
votes
3
replies
1.2k
views
Limma comparing gene expression between base line and one treatment
limma
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
AL
• 0
0
votes
1
reply
1.3k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
picasa1983
• 0
2
votes
5
replies
1.3k
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
sop
• 0
4
votes
14
replies
2.8k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Michael E
• 0
3
votes
4
replies
1.4k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
20 months ago
jcollier
• 0
4
votes
4
replies
1.9k
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
20 months ago
sukeshinik5
▴ 20
0
votes
1
reply
633
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Neha
• 0
4
votes
4
replies
1.3k
views
Warning message when running limma with covariates
limma
20 months ago • updated 14 months ago
Chris
▴ 20
4,232 results • Page
2 of 85
Recent ...
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Answer: Unable to find ENTREZ IDs
by
James W. MacDonald
68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql
by
a2a2hd42aa
• 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
by
A.Barden
▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
by
Gordon Smyth
53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack
by
a2a2hd42aa
• 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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