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limma
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reset
1
vote
2
replies
84
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 2 hours ago
Anna
• 0
1
vote
2
replies
284
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
11 days ago • updated 10 days ago
Dylan.Sheerin
• 0
2
votes
2
replies
286
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
12 days ago • updated 7 days ago
zzrammal
• 0
3
votes
10
replies
484
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Abbey
• 0
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
Kim
• 0
0
votes
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
c53aba27
• 0
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA
limma
20 days ago • updated 19 days ago
Chris
▴ 10
0
votes
3
replies
282
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
SSSJec
• 0
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 27 days ago by
taur.vil
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 18 days ago
Chris
▴ 10
0
votes
2
replies
245
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 weeks ago • updated 28 days ago
catv
• 0
5
votes
3
replies
318
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
7
replies
366
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 27 days ago
hortense96
• 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 20 days ago
Chris
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 12 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 27 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 19 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 19 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
18 results • Page
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Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Answer: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
by
James W. MacDonald
65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Votes
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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