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limma
•
reset
3
votes
4
replies
156
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
0
votes
3
replies
196
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
1
reply
130
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 9 days ago by
Gordon Smyth
50k • 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 9 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 11 hours ago
Chris
• 0
3
votes
1
reply
156
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
285
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
14 days ago • updated 8 days ago
hortense96
• 0
1
vote
3
replies
340
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 21 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
382
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 25 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
0
votes
4
replies
301
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 28 days ago by
jari.karppinen
• 0
0
votes
2
replies
182
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
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
515
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
862
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
443
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
230
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
385
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 • updated 6 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
494
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago • updated 7 weeks ago
dl17032000
• 0
8
votes
6
replies
445
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
293
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
299
views
Bioconductor unreachable?
limma
9 weeks ago
edoardo
• 0
0
votes
9
replies
549
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 10 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
361
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 • updated 11 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
580
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: 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…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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