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LIMMA
•
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2
votes
2
replies
997
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 50 minutes ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 58 minutes ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
3
votes
3
replies
54
views
Help with error using camera() in limma
CAMERA
limma
updated 1 hour ago by
James W. MacDonald
65k • written 4 hours ago by
Chris
• 0
0
votes
3
replies
161
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 hours ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 3 hours ago
Chris
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 4 hours ago
Chris
• 0
0
votes
7
replies
281
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
13 days ago • updated 7 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 7 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
0
votes
1
reply
123
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
taur.vil
• 0
0
votes
2
replies
182
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
11 days ago • updated 8 days ago
catv
• 0
3
votes
1
reply
150
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
Shaimaa Gamal
• 0
5
votes
9
replies
886
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
19 days ago • updated 12 days ago
Chris
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 12 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
586
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 14 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
3
replies
334
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 15 days ago by
Gordon Smyth
50k • written 20 days ago by
Simran
• 0
2
votes
6
replies
371
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
22 days ago • updated 21 days ago
Chris
• 0
0
votes
4
replies
296
views
Help with design.matrix
limma
25 days ago • updated 24 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
153
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 24 days ago by
Gordon Smyth
50k • written 24 days ago by
avery
• 0
1
vote
4
replies
421
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 25 days ago by
Gordon Smyth
50k • written 27 days ago by
jari.karppinen
• 0
5
votes
25
replies
844
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 25 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
179
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
27 days ago
Gimena
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
22 results • Page
1 of 1
Recent ...
Replies
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
Votes
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
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James W. MacDonald
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jeffrey.maurer
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Chris
• 0
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Leonard Goldstein
▴ 200
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Matthew Ritchie
▴ 1000
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