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limma
•
reset
3
votes
4
replies
162
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
0
votes
3
replies
200
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
2
replies
144
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
0
votes
2
replies
192
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
12 days ago • updated 10 days ago
catv
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 18 hours ago
Chris
• 0
3
votes
1
reply
158
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
287
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
1
vote
3
replies
342
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
5
votes
9
replies
896
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 13 days ago
Chris
• 0
2
votes
6
replies
385
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
23 days ago
Chris
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
0
votes
4
replies
302
views
Help with design.matrix
limma
26 days ago • updated 25 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
426
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
jari.karppinen
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago • updated 28 days ago
Gimena
• 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 1 day ago
Chris
• 0
2
votes
8
replies
517
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
5
votes
25
replies
865
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
7
votes
6
replies
446
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
1
reply
231
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
scoops_streams_06
• 0
0
votes
4
replies
386
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
6 weeks ago • updated 5 weeks ago
Efra
• 0
5
votes
7
replies
447
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
2
votes
2
replies
256
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
7 weeks ago
Sabiha
▴ 20
0
votes
2
replies
258
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
7 weeks ago • updated 6 weeks ago
kcarey
• 0
1
vote
3
replies
394
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
2
votes
6
replies
476
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
8 weeks ago • updated 5 weeks ago
Lily Cheang
▴ 10
3
votes
8
replies
495
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago • updated 7 weeks ago
dl17032000
• 0
8
votes
6
replies
448
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
0
votes
0
replies
148
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
3
replies
278
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Laura
• 0
0
votes
4
replies
294
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
9 weeks ago • updated 8 weeks ago
mperalc
• 0
3
votes
5
replies
615
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
2
votes
1
reply
259
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
1
vote
2
replies
300
views
Bioconductor unreachable?
limma
9 weeks ago
edoardo
• 0
0
votes
9
replies
550
views
limma fo continous variables
limma
DEGseq
updated 9 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
mia
• 0
0
votes
2
replies
283
views
limma model matrix questions
limmaGUI
limma
pairedsamples
10 weeks ago
whyw6948
• 0
0
votes
2
replies
312
views
Limma with replicates at different time points
RNAs
limma
Differen
10 weeks ago • updated 9 weeks ago
alessandro
• 0
2
votes
1
reply
290
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
342
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
363
views
limma with interaction term
R
biostatistics
limma
Epigenetics
11 weeks ago • updated 9 weeks ago
Jitendra
▴ 10
3
votes
2
replies
288
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
12 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
322
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago • updated 11 weeks ago
COPD_Project
• 0
2
votes
2
replies
282
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
12 weeks ago
SamGG
▴ 350
1
vote
4
replies
402
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Jitendra
▴ 10
4
votes
3
replies
348
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
363
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 12 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
0
votes
2
replies
252
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
12 weeks ago
Lily Cheang
▴ 10
1
vote
2
replies
336
views
Longitudinal analysis in Limma
limma
3 months ago
COPD_Project
• 0
2
votes
2
replies
291
views
Using limma for controlling age variable
linearmodeling
limma
3 months ago
Matej
• 0
4
votes
6
replies
581
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 12 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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