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limma
•
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15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 3 days ago
Chris
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 2 days ago
Chris
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 16 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
25
replies
901
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 29 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
5
votes
9
replies
914
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 16 days ago
Chris
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 11 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
3
votes
4
replies
189
views
Help with error using camera() in limma
CAMERA
limma
3 days ago
Chris
• 0
3
votes
1
reply
167
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
Shaimaa Gamal
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 3 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
2
votes
6
replies
397
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
25 days ago
Chris
• 0
1
vote
4
replies
438
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
jari.karppinen
• 0
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 19 days ago by
Gordon Smyth
50k • written 24 days ago by
Simran
• 0
1
vote
2
replies
257
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 14 hours ago by
Gordon Smyth
50k • written 17 hours ago by
Kim
• 0
0
votes
2
replies
154
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 11 days ago by
taur.vil
• 0
0
votes
1
reply
77
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
c53aba27
• 0
0
votes
2
replies
208
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
14 days ago • updated 12 days ago
catv
• 0
0
votes
4
replies
595
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 17 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 3 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
7
replies
309
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
17 days ago • updated 11 days ago
hortense96
• 0
0
votes
4
replies
306
views
Help with design.matrix
limma
28 days ago • updated 27 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
162
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
avery
• 0
0
votes
3
replies
223
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 3 days ago by
James W. MacDonald
65k • written 5 days ago by
SSSJec
• 0
22 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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