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Showing :
Limma
•
reset
0
votes
2
replies
73
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
1 day ago • updated 6 hours ago
Efra
• 0
0
votes
3
replies
97
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 hour ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
2
votes
2
replies
140
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 days ago • updated 4 days ago
Sabiha
▴ 20
0
votes
2
replies
125
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 0
0
votes
3
replies
276
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 6 weeks ago by
pl23
• 0
0
votes
5
replies
248
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Lily Cheang
• 0
3
votes
8
replies
379
views
Constrast for Time Course Experiments using Limma
limma
13 days ago • updated 11 days ago
dl17032000
• 0
8
votes
6
replies
314
views
DGE analysis with LIMMA
limma
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
Amit
• 0
0
votes
0
replies
104
views
Can I combine collinear variables into a single value
BatchEffect
limma
18 days ago
Harrsha
• 0
0
votes
3
replies
196
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 12 days ago by
Gordon Smyth
50k • written 20 days ago by
Laura
• 0
0
votes
4
replies
194
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
20 days ago • updated 18 days ago
mperalc
• 0
3
votes
5
replies
486
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 14 days ago by
Michael Love
41k • written 24 days ago by
sap275
▴ 10
2
votes
1
reply
179
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
sap275
▴ 10
1
vote
2
replies
199
views
Bioconductor unreachable?
limma
25 days ago
edoardo
• 0
0
votes
9
replies
378
views
limma fo continous variables
limma
DEGseq
updated 21 days ago by
James W. MacDonald
65k • written 26 days ago by
mia
• 0
0
votes
2
replies
217
views
limma model matrix questions
limmaGUI
limma
pairedsamples
28 days ago
whyw6948
• 0
0
votes
2
replies
251
views
Limma with replicates at different time points
RNAs
limma
Differen
4 weeks ago • updated 21 days ago
alessandro
• 0
2
votes
1
reply
228
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 3.9k • written 4 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
277
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
265
views
limma with interaction term
R
biostatistics
limma
Epigenetics
5 weeks ago • updated 22 days ago
Jitendra
▴ 10
3
votes
2
replies
200
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
5 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
227
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
5 weeks ago
COPD_Project
• 0
2
votes
2
replies
216
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
5 weeks ago
SamGG
▴ 330
1
vote
4
replies
271
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
4
votes
3
replies
239
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
275
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
966
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 10 months ago by
informatician
• 0
0
votes
2
replies
191
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
6 weeks ago
Lily Cheang
• 0
1
vote
2
replies
245
views
Longitudinal analysis in Limma
limma
6 weeks ago
COPD_Project
• 0
2
votes
2
replies
196
views
Using limma for controlling age variable
linearmodeling
limma
7 weeks ago
Matej
• 0
4
votes
6
replies
467
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 5 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Shaimaa Gamal
• 0
0
votes
5
replies
428
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 10 weeks ago by
ATpoint
★ 3.9k • written 10 weeks ago by
Xiao
• 0
2
votes
4
replies
423
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 10 weeks ago by
Gordon Smyth
50k • written 3 months ago by
michelafrancesconi8
• 0
1
vote
2
replies
411
views
Assess fit of variance prior
limma
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Frederik Ziebell
▴ 20
2
votes
1
reply
239
views
removeBatchEffect with non-linear model fit
limma
DESeq2
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
georgii.vdovin
• 0
2
votes
4
replies
516
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
kyj2226
• 0
0
votes
3
replies
335
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip
limma
goana
updated 3 months ago by
SamGG
▴ 330 • written 3 months ago by
samagbeyimodupe
• 0
5
votes
2
replies
436
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
7
votes
2
replies
575
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
0
votes
0
replies
167
views
multipollutant models
statistics
Regression
r
limma
3 months ago
Jitendra
▴ 10
0
votes
3
replies
385
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
3 months ago
Karthik
• 0
1
vote
1
reply
316
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
michael.eigenschink
• 0
3
votes
4
replies
453
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
3 months ago
pl23
• 0
2
votes
4
replies
534
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
4 months ago
Tyler Sagendorf
▴ 10
1
vote
4
replies
542
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
0
votes
2
replies
423
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
4 months ago
Crystal571
• 0
0
votes
5
replies
739
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
e.vanzanten.1
• 0
0
votes
5
replies
798
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
5 months ago
dorota.komar
• 0
0
votes
1
reply
398
views
Issue with weights in voomLmFit()
limma
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
gabriel.hoffman
▴ 100
2
votes
1
reply
777
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor
biocon
limma
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
ningyuan
• 0
50 results • Page
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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