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Showing :
Limma
•
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1
vote
1
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54
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 1 day ago by
ATpoint
★ 1.2k • written 1 day ago by
Dimitris
• 0
1
vote
4
replies
100
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 1 day ago by
Kevin Blighe
3.5k • written 2 days ago by
beslinail
• 0
3
votes
3
replies
111
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 1 day ago by
Gordon Smyth
45k • written 2 days ago by
mohammedtoufiq91
▴ 10
0
votes
6
replies
134
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
2 days ago • updated 1 day ago
nabiyogesh
▴ 10
0
votes
2
replies
96
views
Using limma to read Illumina HT-12 v4 data
limma
updated 4 days ago by
Gordon Smyth
45k • written 4 days ago by
orbitofrontal
• 0
3
votes
4
replies
131
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
7 days ago • updated 6 days ago
Yang Shi
• 0
4
votes
6
replies
191
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
7 days ago • updated 2 days ago
mohammedtoufiq91
▴ 10
2
votes
2
replies
103
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 11 days ago by
Gordon Smyth
45k • written 11 days ago by
dr
▴ 10
1
vote
2
replies
82
views
toptable sort .by set
limma
rnaseqGene
12 days ago
snowmattin
• 0
1
vote
5
replies
187
views
Unsuccessful DE analysis using limma - voom
limma
14 days ago • updated 13 days ago
loainaom
• 0
2
votes
1
reply
99
views
Extremely low P-values when using Limma on high sample size proteomics data
limma
Proteomics
updated 15 days ago by
James W. MacDonald
59k • written 15 days ago by
roger.moreno.justicia
• 0
2
votes
1
reply
67
views
Limma model orientation
limma
methylation
MethylationArray
updated 20 days ago by
James W. MacDonald
59k • written 20 days ago by
fluentin44
• 0
2
votes
4
replies
158
views
Overfitting in limma
limma
Regression
overfitting
updated 14 days ago by
Gordon Smyth
45k • written 20 days ago by
M.Gierlinski
• 0
0
votes
0
replies
59
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma
diffcyt
edgeR
25 days ago
stefanos.bamopoulos
• 0
0
votes
3
replies
106
views
Limma time course with several conditions
limma
28 days ago • updated 27 days ago
rina
▴ 20
1
vote
4
replies
229
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma
voom
updated 28 days ago by
Gordon Smyth
45k • written 4 weeks ago by
jmannhei
▴ 10
0
votes
7
replies
287
views
Which Limma guide is recommended ?
limma
R
DifferentialExpression
5 weeks ago • updated 21 days ago
loainaom
• 0
0
votes
2
replies
153
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
5 weeks ago
Wendy
• 0
3
votes
4
replies
212
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
6 weeks ago
mohammedtoufiq91
▴ 10
2
votes
2
replies
166
views
Limma vs. lm for methylation data
limma
MethylationArrayData
MethylationArray
6 weeks ago • updated 5 weeks ago
fluentin44
• 0
1
vote
6
replies
253
views
Differential expression analysis - Clariom S array -workflow
design-matrix
limma
7 weeks ago
ala
• 0
0
votes
1
reply
125
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq
RNASeqData
limma
limmaGUI
updated 7 weeks ago by
Michael Love
37k • written 7 weeks ago by
sushimoto
• 0
1
vote
4
replies
208
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
8 weeks ago • updated 7 weeks ago
sushimoto
• 0
1
vote
3
replies
156
views
how to change axis labeling in limma density plot
desnity
limma
updated 8 weeks ago by
Gordon Smyth
45k • written 8 weeks ago by
adR
▴ 10
0
votes
4
replies
242
views
How to model a pre and post treatment in limma
limma
8 weeks ago
AST
▴ 50
0
votes
4
replies
227
views
limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq
limma
9 weeks ago • updated 8 weeks ago
danphillips28
• 0
6
votes
2
replies
167
views
The number of controls versus treatment in differential expression analysis
DESeq2
edgeR
limma
updated 9 weeks ago by
Gordon Smyth
45k • written 9 weeks ago by
AZ
▴ 30
0
votes
0
replies
120
views
Differences between limma and edgeR
limma
9 weeks ago
jose.carmeliet
• 0
4
votes
2
replies
153
views
Covariates to be included in DE model
DESeq2
limma
updated 9 weeks ago by
Gordon Smyth
45k • written 9 weeks ago by
forlani.luca
• 0
0
votes
9
replies
353
views
Handling of missing values in limma
limma
missingValues
updated 6 days ago by
Gordon Smyth
45k • written 10 weeks ago by
Arend
• 0
0
votes
1
reply
164
views
Limma interaction term
RNASeqData
limma
DifferentialExpression
updated 10 weeks ago by
Gordon Smyth
45k • written 10 weeks ago by
bageerathan.v
• 0
2
votes
2
replies
184
views
Complex contrasts in limma
RNASeq
limma
DifferentialExpression
11 weeks ago
tcalvo
▴ 70
0
votes
3
replies
196
views
limma voom contrasts
contrasts
limma
voom
updated 11 weeks ago by
Gordon Smyth
45k • written 11 weeks ago by
S T
▴ 80
0
votes
6
replies
418
views
how plotSA shall look like for good or bad data, any example of good or bad data shall look like in plotSA regarding whether the data is OK for limma…
plotSA
limma
11 weeks ago
Ming
▴ 360
2
votes
3
replies
221
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma
DifferentialExpression
12 weeks ago
nhaus
• 0
2
votes
1
reply
194
views
DESeq2 handling of replicates
DESeq2
RNASeq
limma
updated 3 months ago by
Michael Love
37k • written 3 months ago by
Eyal
• 0
0
votes
3
replies
268
views
Need help with a contrast design for limma with a missing group?
limma
VOOM
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
Ahdee
▴ 50
1
vote
1
reply
180
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 3 months ago by
ATpoint
★ 1.2k • written 3 months ago by
nhaus
• 0
0
votes
1
reply
191
views
Running limma in parallel
parallel
R
limma
EWAS
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
Lorenzo
• 0
4
votes
5
replies
388
views
What to do if covariates in design matrix of limma are confounded
limma
DifferentialExpression
updated 23 days ago by
Sneha
• 0 • written 3 months ago by
nhaus
• 0
3
votes
6
replies
484
views
Unable to install "limma" package on RStudio
Bioconductor
limma
limmaGUI
3 months ago
jaydengitt
• 0
5
votes
5
replies
320
views
Where to find old limma packages not part of a Bioc release?
archive
limma
3 months ago
Jonathan
• 0
0
votes
1
reply
173
views
How to design limma for two populations from each tumor, multiple tumors from several of the patients
limma
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
JMINCHAN
• 0
0
votes
2
replies
270
views
Limma Differential Analysis on Proteomics data
Proteomics
limma
Limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
Mrinal.singh06
• 0
0
votes
4
replies
333
views
How do you get averages of each group in Limma output
RNASeq
limma
3 months ago
Matthew
• 0
4
votes
3
replies
301
views
Limma/voom analysis of time-series data (with only 1 condition)
limma
DifferentialExpression
updated 3 months ago by
James W. MacDonald
59k • written 3 months ago by
annaschumannuni
• 0
1
vote
4
replies
293
views
Phosphoproteomics time series analysis with splines
limma
splines
4 months ago
rina
▴ 20
1
vote
1
reply
421
views
Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
limma
updated 4 months ago by
Gordon Smyth
45k • written 4 months ago by
keervanik
• 0
0
votes
0
replies
128
views
Complex design in DESeq2 doesn't seem to be supported in Glimma
limma
Glimma
RNASeq
DESeq2
4 months ago
Jonas
• 0
2
votes
2
replies
989
views
EdgeR installation issue
limma
edgeR
DESeq2
4 months ago
aonghus
• 0
50 results • Page
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
by
Lan Anh
• 0
Hello, Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the h…
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Thanks, Dr. Smyth!
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Oops. I just corrected the URL. Thank you Dr. Smyth.
Comment: Fail to run RupRadar
by
Qingwei
• 0
Dear Sergi, Yeah, it works. ```r dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads, GTF.featureType="cDNA_match", GTF.attrType="ID…
Comment: LogFC values in edgeR - w/wo intercept
by
Gordon Smyth
45k
The link you've entered for "A guide to creating design matrices for gene expression experiments" doesn't work. Could you please correct th…
Votes
Comment: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: broken chain import in liftOver
Answer: toGRanges help!
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