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Showing :
limma
•
reset
0
votes
3
replies
142
views
Extract Limma Adjusted Values for Plotting
limma
updated 2 days ago by
ATpoint
★ 2.9k • written 3 days ago by
phelankj
• 0
3
votes
6
replies
264
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 5 days ago by
Gordon Smyth
47k • written 6 days ago by
mohammedtoufiq91
▴ 10
1
vote
2
replies
158
views
Extracting fitted expression matrix from Limma
limma
10 days ago • updated 8 days ago
sarah.kelliher
• 0
3
votes
11
replies
457
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
10 days ago • updated 1 day ago
Anna
▴ 20
0
votes
2
replies
98
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
12 days ago
pg45863
• 0
0
votes
5
replies
236
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
13 days ago • updated 12 days ago
pg45863
• 0
0
votes
1
reply
132
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 12 days ago by
swbarnes2
★ 1.2k • written 13 days ago by
simon
• 0
0
votes
1
reply
144
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression
limma
updated 24 days ago by
Gordon Smyth
47k • written 24 days ago by
mbyvcm
• 0
3
votes
4
replies
228
views
Anova table edgeR limma
limma
RNASeq
edgeR
25 days ago • updated 24 days ago
KATHERINE CHUERE NUNES
• 0
0
votes
2
replies
169
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 4 weeks ago by
informatician
• 0
1
vote
2
replies
137
views
Contrast of Contrasts in Limma
limma
DifferentialExpression
28 days ago • updated 27 days ago
mpitz
• 0
1
vote
3
replies
220
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower
edgeR
DifferentialExpression
limma
RNASeq
updated 4 weeks ago by
Gordon Smyth
47k • written 4 weeks ago by
Sara
• 0
0
votes
0
replies
115
views
Volcano plot
limma
AffymetrixChip
4 weeks ago
e.gunaut
• 0
0
votes
2
replies
194
views
Limma multi-group, nested analysis with aggregation
limma
5 weeks ago • updated 4 weeks ago
Jonathan
• 0
0
votes
1
reply
160
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 5 weeks ago by
Gordon Smyth
47k • written 5 weeks ago by
qiz218591
• 0
2
votes
3
replies
262
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma
CustomCDF
Affyhgu133aExpr
limma
affy
updated 7 weeks ago by
James W. MacDonald
63k • written 7 weeks ago by
Pratik Mehta
▴ 10
1
vote
2
replies
204
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
7 weeks ago
Abdul
▴ 20
2
votes
2
replies
267
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
8 weeks ago
Abdul
▴ 20
0
votes
2
replies
218
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
9 weeks ago • updated 5 weeks ago
qiz218591
• 0
0
votes
2
replies
164
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 9 weeks ago by
Gordon Smyth
47k • written 9 weeks ago by
Ankita
• 0
1
vote
4
replies
816
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
2.7 years ago • updated 9 weeks ago
linouhao
▴ 20
2
votes
4
replies
269
views
limma with or without intercept gives different results
limma
rnaseq
10 weeks ago • updated 9 weeks ago
Sydney
• 0
0
votes
1
reply
149
views
Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 10 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
S
• 0
0
votes
3
replies
296
views
[limma::kegga] Pathway names all NA
KEGG
limma
updated 10 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
andrewsm
• 0
0
votes
1
reply
150
views
Limma for Fluidigm high throughput PCR
limma
Limma
Fluidigm
updated 10 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
jms2520
• 0
1
vote
4
replies
255
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 10 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
Yang Shi
▴ 10
2
votes
7
replies
402
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 11 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
Constantin Ahlmann-Eltze
▴ 30
0
votes
0
replies
101
views
Limma: Models containing an intercept and interactions with continuous variables.
limma
edgeR
DifferentialExpression
11 weeks ago
Aashil
• 0
0
votes
0
replies
201
views
Some questions regarding using limma and interpretation
limma
11 weeks ago
Sep
• 0
1
vote
2
replies
169
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
12 weeks ago • updated 11 weeks ago
Yang Shi
▴ 10
0
votes
1
reply
153
views
specifying comparison of interest in the minfi Bumhunter function
limma
bumphunter
methylationArrayAnalysis
minfi
updated 12 weeks ago by
James W. MacDonald
63k • written 12 weeks ago by
edward.esiribloom
• 0
2
votes
2
replies
197
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 12 weeks ago by
Gordon Smyth
47k • written 12 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
220
views
Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma
RNASeqData
edgeR
updated 3 months ago by
Hilary
▴ 30 • written 3 months ago by
Lucas
• 0
0
votes
1
reply
202
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 3 months ago by
Kevin Blighe
3.8k • written 3 months ago by
Joshua
• 0
1
vote
3
replies
245
views
Calculating the contrast of two genotypes "vs"
limma
updated 3 months ago by
Gordon Smyth
47k • written 3 months ago by
Wuschel
▴ 10
0
votes
17
replies
635
views
How to check linear model
modalmatrix
limma
R
linear
3 months ago
Jitendra
▴ 10
6
votes
11
replies
569
views
Error in running Dispersion estimation analysis in EdgeR
edgeR
DifferentialExpression
limma
design
RNASeq
3 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
249
views
Differential expression analysis with global differences among samples (tissues)
DESeq2
qsmooth
edgeR
limma
updated 3 months ago by
Gordon Smyth
47k • written 3 months ago by
Gregory
• 0
5
votes
2
replies
289
views
Sva and batch effect
limma
BatchEffect
sva
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
Lenny186
• 0
1
vote
3
replies
244
views
Limma-voom with inverse probability weights (similar to sample weights)
limma
limma-voom
StatisticalMethod
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
jay
• 0
2
votes
4
replies
275
views
Reproducibility using limma for DE Analysis
limma
seed
DifferentialRegulation
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
TSauer
• 0
4
votes
1
reply
397
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 4 months ago by
ATpoint
★ 2.9k • written 4 months ago by
luca.s
▴ 40
3
votes
5
replies
427
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 4 months ago by
Michael Love
40k • written 4 months ago by
aditya.m
▴ 10
0
votes
1
reply
989
views
limma: decideTests
affy
limma
affy
limma
updated 4 months ago by
Gordon Smyth
47k • written 15.5 years ago by
Al Ivens
▴ 270
0
votes
1
reply
168
views
NAs in some genes in topTable output
limma
topTable
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
thkapell
▴ 10
0
votes
1
reply
173
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
wiscoyogi
• 0
0
votes
2
replies
393
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
Keith
• 0
3
votes
4
replies
373
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 4 months ago by
Gordon Smyth
47k • written 4 months ago by
Edmond
• 0
2
votes
2
replies
257
views
Estimating Fold-Changes of Lowly Expressed Genes
limma
4 months ago
vm
▴ 30
0
votes
2
replies
284
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
4 months ago
dqt
• 0
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Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Bruno
• 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output
by
betterwound
• 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub?
by
Bruno
• 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable
by
swbarnes2
★ 1.2k
Did you relevel before or after calling DESeq?
Votes
Comment: DESeq2 on multilevel design variable
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
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