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Showing :
limma
•
reset
2
votes
2
replies
263
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago
zzrammal
• 0
3
votes
10
replies
433
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 6 days ago by
James W. MacDonald
65k • written 9 days ago by
Abbey
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 6 days ago by
Gordon Smyth
50k • written 28 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
248
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
8 days ago • updated 7 days ago
Dylan.Sheerin
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 9 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
Kim
• 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
c53aba27
• 0
0
votes
2
replies
189
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 24 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
26 days ago • updated 15 days ago
Chris
▴ 10
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA
limma
16 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 16 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 16 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
3
replies
270
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 16 days ago
Chris
▴ 10
0
votes
7
replies
352
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
29 days ago • updated 23 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 23 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
0
votes
2
replies
236
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
27 days ago • updated 24 days ago
catv
• 0
5
votes
9
replies
972
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 28 days ago
Chris
▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 29 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
628
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 4 weeks ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Simran
• 0
2
votes
6
replies
451
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
5 weeks ago
Chris
▴ 10
0
votes
4
replies
329
views
Help with design.matrix
limma
5 weeks ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
185
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
avery
• 0
1
vote
4
replies
461
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
5
votes
25
replies
985
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
206
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 weeks ago
Gimena
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
2
votes
8
replies
559
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
7
replies
481
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
0
votes
4
replies
408
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
8 weeks ago • updated 7 weeks ago
Efra
• 0
2
votes
6
replies
548
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
10 weeks ago • updated 7 weeks ago
Lily Cheang
▴ 10
7
votes
6
replies
478
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
0
votes
1
reply
250
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
2
replies
311
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
9 weeks ago
kcarey
• 0
2
votes
2
replies
288
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
9 weeks ago
Sabiha
▴ 20
1
vote
3
replies
436
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
3
votes
8
replies
539
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago
dl17032000
• 0
0
votes
3
replies
316
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Laura
• 0
3
votes
5
replies
664
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 10
8
votes
6
replies
501
views
DGE analysis with LIMMA
limma
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Amit
• 0
0
votes
0
replies
163
views
Can I combine collinear variables into a single value
BatchEffect
limma
10 weeks ago
Harrsha
• 0
0
votes
4
replies
322
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
0
votes
2
replies
345
views
Limma with replicates at different time points
RNAs
limma
Differen
3 months ago • updated 11 weeks ago
alessandro
• 0
0
votes
9
replies
588
views
limma fo continous variables
limma
DEGseq
updated 11 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
mia
• 0
2
votes
1
reply
276
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 10
0
votes
4
replies
390
views
limma with interaction term
R
biostatistics
limma
Epigenetics
3 months ago • updated 11 weeks ago
Jitendra
▴ 10
1
vote
2
replies
337
views
Bioconductor unreachable?
limma
12 weeks ago
edoardo
• 0
0
votes
2
replies
314
views
limma model matrix questions
limmaGUI
limma
pairedsamples
12 weeks ago
whyw6948
• 0
2
votes
1
reply
318
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
50 results • Page
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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