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Showing :
RnaSeq
•
reset
1
vote
2
replies
169
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
7 days ago • updated 6 days ago
drewhaydensteele
• 0
3
votes
2
replies
186
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 10 days ago by
Gordon Smyth
49k • written 10 days ago by
annikagable
• 0
0
votes
3
replies
196
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
18 days ago • updated 10 days ago
Karthik
• 0
0
votes
1
reply
171
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 13 days ago by
Michael Love
41k • written 16 days ago by
pl23
• 0
2
votes
3
replies
168
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
17 days ago • updated 12 days ago
Karthik
• 0
2
votes
2
replies
186
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
20 days ago • updated 19 days ago
Manthos
• 0
2
votes
4
replies
315
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
25 days ago • updated 24 days ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
227
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 7 weeks ago by
Sean
• 0
0
votes
2
replies
242
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 4 weeks ago by
Leonardo Collado Torres
★ 1.0k • written 6 weeks ago by
tangming2005
▴ 190
0
votes
9
replies
2.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 4 weeks ago by
blowfish
• 0 • written 6.1 years ago by
bharata1803
▴ 60
1
vote
4
replies
356
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
5 weeks ago
Wending
• 0
0
votes
0
replies
146
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 weeks ago
mch
• 0
4
votes
2
replies
269
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 weeks ago by
Gordon Smyth
49k • written 6 weeks ago by
alvaroperona1
▴ 10
0
votes
6
replies
395
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 weeks ago
erika.maldonado-rosado
• 0
0
votes
0
replies
155
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
7 weeks ago
Sara
• 0
0
votes
2
replies
418
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
7 weeks ago • updated 6 weeks ago
Karthik
• 0
0
votes
0
replies
143
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
7 weeks ago
Florian
• 0
0
votes
0
replies
142
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
7 weeks ago
Xinqi
• 0
0
votes
0
replies
153
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
7 weeks ago
Sara
• 0
1
vote
1
reply
233
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 7 weeks ago by
James W. MacDonald
64k • written 7 weeks ago by
fuqichen1
• 0
1
vote
7
replies
485
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 6 days ago by
Gordon Smyth
49k • written 8 weeks ago by
Gimena
• 0
0
votes
2
replies
240
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 8 weeks ago by
swbarnes2
★ 1.3k • written 8 weeks ago by
Jules
• 0
0
votes
1
reply
244
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 9 weeks ago by
Basti
▴ 740 • written 10 weeks ago by
Luke
• 0
3
votes
5
replies
405
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 12 weeks ago by
ATpoint
★ 3.6k • written 12 weeks ago by
Shashank
• 0
1
vote
1
reply
251
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 3 months ago by
ATpoint
★ 3.6k • written 3 months ago by
jg0428
• 0
0
votes
1
reply
397
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
Adam
• 0
1
vote
6
replies
562
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 3 months ago by
ATpoint
★ 3.6k • written 3 months ago by
Debebe
• 0
5
votes
7
replies
485
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 4 months ago by
Gordon Smyth
49k • written 4 months ago by
Jonathan
▴ 10
0
votes
1
reply
792
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 4 months ago by
James W. MacDonald
64k • written 4 months ago by
chiwut.wong
• 0
2
votes
1
reply
426
views
Grouping DEGs yields varying results
RNASeq
limma
updated 4 months ago by
Gordon Smyth
49k • written 4 months ago by
Jonathan
▴ 10
2
votes
5
replies
764
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
4 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
450
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression
RNASeq
DESeq2
4 months ago
Matteo
• 0
3
votes
2
replies
649
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 5 months ago by
Gordon Smyth
49k • written 5 months ago by
Jonathan
▴ 10
0
votes
3
replies
421
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 5 months ago by
James W. MacDonald
64k • written 5 months ago by
a26fd14e
• 0
3
votes
11
replies
1.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
6 months ago
Anna
▴ 20
1
vote
9
replies
4.7k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 5.8 years ago by
klalit1803
• 0
0
votes
1
reply
406
views
CI for logCPM (fitted values)
RNAseq
edgeR
updated 6 months ago by
Gordon Smyth
49k • written 6 months ago by
HS
▴ 10
3
votes
4
replies
539
views
Anova table edgeR limma
limma
RNASeq
edgeR
7 months ago
KATHERINE CHUERE NUNES
• 0
1
vote
2
replies
440
views
Obtention of the binomial transformed count table with edgeR
DESeq2
edgeR
RNASeq
DifferentialExpression
updated 7 months ago by
Gordon Smyth
49k • written 7 months ago by
Sofía
• 0
0
votes
3
replies
567
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 7 months ago by
Michael Love
41k • written 7 months ago by
Alberto
• 0
0
votes
2
replies
606
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 7 months ago by
informatician
• 0
1
vote
3
replies
567
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower
edgeR
DifferentialExpression
limma
RNASeq
updated 7 months ago by
Gordon Smyth
49k • written 7 months ago by
Sara
• 0
0
votes
2
replies
694
views
model matrix not full rank
DESeq2
RNASeq
updated 7 months ago by
garryfrenchgarry
• 0 • written 7 months ago by
Simran
• 0
0
votes
1
reply
353
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2
RNASeq
updated 7 months ago by
Michael Love
41k • written 8 months ago by
rohanphn
• 0
2
votes
3
replies
413
views
RNA seq with edgeR with several factors
RNAseq
factors
7 months ago
Nathalie
▴ 20
0
votes
3
replies
600
views
edgeR DEGs multilevel
edgeR
RNASeq
DifferentialRegulation
updated 7 months ago by
Gordon Smyth
49k • written 7 months ago by
bioinfoWanderer
• 0
7
votes
8
replies
10.0k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 7 months ago by
ATpoint
★ 3.6k • written 7.4 years ago by
EJ
▴ 20
0
votes
4
replies
570
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 7 months ago by
swbarnes2
★ 1.3k • written 7 months ago by
Young Tae
• 0
1
vote
1
reply
401
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2
edgeR
RNAseq
updated 7 months ago by
Gordon Smyth
49k • written 7 months ago by
cmareevicars
• 0
3
votes
12
replies
1.0k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 7 months ago by
Michael Love
41k • written 7 months ago by
urwah
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Can the limma package be applied to Log2 RUV-normalized data?
by
Gordon Smyth
49k
515 samples is certainly large enough.
Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
• 0
Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim
Comment: Agilent Microarray Gene Oncology analysis gone wrong
by
SamGG
▴ 320
Gordon said to let coef to its default value: topTable(fit, n=20)
Comment: Can the limma package be applied to Log2 RUV-normalized data?
by
Shaimaa Gamal
• 0
Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…
Comment: Agilent Microarray Gene Oncology analysis gone wrong
by
samagbeyimodupe
• 0
Thank you for the quick response. i ran the codes again and removed all the other arguments for eBayes except for fit. I ran the line of co…
Votes
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
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