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tmm
•
reset
5
votes
2
replies
685
views
PhD student
TMM
limma
10 months ago
Nisha
• 0
1
vote
1
reply
768
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
tleona3
• 0
1
vote
4
replies
1.1k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 19 months ago by
Simon Pearce
• 0 • written 19 months ago by
a.riediger
▴ 20
1
vote
1
reply
834
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
e.g.w.miller
▴ 10
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.1 years ago by
maria.soler
• 0
2
votes
1
reply
1.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
BioNovice247
• 0
0
votes
2
replies
935
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR
DifferentialExpression
TMM
RNASeq
updated 2.6 years ago by
Gordon Smyth
50k • written 2.6 years ago by
hamidrezarazzaghian
• 0
3
votes
2
replies
867
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 4.1 years ago by
Rory Stark
★ 5.2k • written 4.1 years ago by
Guandong Shang
▴ 40
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.7 years ago
ATpoint
★ 4.1k
1
vote
1
reply
880
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma
TMM
differential expression
normalization
rnaseq
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
natalia_lt
• 0
1
vote
4
replies
1.7k
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 5.3 years ago by
Gordon Smyth
50k • written 5.4 years ago by
rproendo
▴ 20
6
votes
7
replies
1.9k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 5.4 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 5.4 years ago by
Konstantinos Yeles
▴ 80
1
vote
4
replies
2.1k
views
processing of (salmon) gene counts for eqtl analysis
salmon
tximport
gene length
eqtl
TMM
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
VSM
▴ 120
0
votes
1
reply
1.1k
views
Limit on significant genes for TMM normalization
normalization
quantile normalization
tmm
edger
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
bilcodygm
• 0
3
votes
7
replies
5.8k
views
Limma PlotMDS: what values should be used?
limma
edger
plotmds
tmm
masigpro
6.4 years ago
dacaba.92
▴ 10
6
votes
4
replies
3.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR
tmm
normalization
counts
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
jol.espinoz
▴ 40
2
votes
3
replies
2.5k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression
TMM
normalization
rnaseq
edger
7.1 years ago
aec
▴ 90
2
votes
7
replies
5.3k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
7.2 years ago
kkadzi25
• 0
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 7.3 years ago by
Rory Stark
★ 5.2k • written 7.3 years ago by
siklenkak
• 0
5
votes
4
replies
3.2k
views
Normalization factor in TMM method
TMM
normalization
edgeR
updated 7.6 years ago by
James W. MacDonald
65k • written 7.6 years ago by
Sara
▴ 10
2
votes
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM
edgeR
7.9 years ago
humberto_munoz
• 0
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
7.9 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
1.9k
views
DiffBind TMM normalization
Rory Stark
diffbind
TMM
edgeR
chipseq
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 8.0 years ago by
akdess
• 0
7
votes
12
replies
4.8k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 24 months ago by
Gordon Smyth
50k • written 8.5 years ago by
hamidrezarazzaghian
• 0
4
votes
1
reply
4.7k
views
norm.factors in TMM normalisation
edgr
tmm
normalization
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.6 years ago
nickbern92
• 0
4
votes
3
replies
2.8k
views
TMM Manual Calculation to be used in MATLAB on miRNA count data
matlab
calcnormfactors
TMM
edgeR
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
katherine.beaulieu14
• 0
28 results • Page
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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
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…
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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