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limma
•
reset
1
vote
2
replies
89
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 8 hours ago
Anna
• 0
1
vote
2
replies
286
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
13 days ago • updated 7 days ago
zzrammal
• 0
3
votes
10
replies
488
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 17 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 18 days ago by
c53aba27
• 0
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA
limma
20 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 19 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
319
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
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
1
vote
3
replies
369
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Simran
• 0
2
votes
6
replies
473
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
6 weeks ago
Chris
▴ 10
0
votes
1
reply
187
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
avery
• 0
0
votes
4
replies
333
views
Help with design.matrix
limma
6 weeks ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
463
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
jari.karppinen
• 0
0
votes
2
replies
208
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 weeks ago
Gimena
• 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
2
votes
8
replies
568
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
5
votes
25
replies
993
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 6 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Jitendra
▴ 10
7
votes
6
replies
482
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
0
votes
1
reply
253
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
scoops_streams_06
• 0
0
votes
4
replies
417
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
9 weeks ago • updated 7 weeks ago
Efra
• 0
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 7 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Amit
• 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
9 weeks ago
Sabiha
▴ 20
0
votes
2
replies
320
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
9 weeks ago
kcarey
• 0
2
votes
6
replies
572
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
10 weeks ago • updated 7 weeks ago
Lily Cheang
▴ 10
3
votes
8
replies
548
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago
dl17032000
• 0
8
votes
6
replies
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Amit
• 0
0
votes
0
replies
170
views
Can I combine collinear variables into a single value
BatchEffect
limma
11 weeks ago
Harrsha
• 0
0
votes
3
replies
325
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Laura
• 0
0
votes
4
replies
328
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
2
votes
1
reply
281
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 12 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
3
votes
5
replies
673
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
1
vote
2
replies
352
views
Bioconductor unreachable?
limma
12 weeks ago
edoardo
• 0
0
votes
9
replies
594
views
limma fo continous variables
limma
DEGseq
updated 12 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
mia
• 0
0
votes
2
replies
322
views
limma model matrix questions
limmaGUI
limma
pairedsamples
3 months ago
whyw6948
• 0
0
votes
2
replies
351
views
Limma with replicates at different time points
RNAs
limma
Differen
3 months ago • updated 12 weeks ago
alessandro
• 0
2
votes
1
reply
321
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
391
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
397
views
limma with interaction term
R
biostatistics
limma
Epigenetics
3 months ago • updated 12 weeks ago
Jitendra
▴ 10
3
votes
2
replies
322
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
3 months ago
Shaimaa Gamal
• 0
2
votes
3
replies
352
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago
COPD_Project
• 0
1
vote
4
replies
447
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jitendra
▴ 10
2
votes
2
replies
307
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
3 months ago
SamGG
▴ 350
4
votes
3
replies
385
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
392
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
50 results • Page
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Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
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
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