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tmm
•
reset
5
votes
2
replies
741
views
PhD student
TMM
limma
11 months ago
Nisha
• 0
1
vote
1
reply
827
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 16 months ago by
Gordon Smyth
51k • written 16 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 21 months ago by
Simon Pearce
• 0 • written 21 months ago by
a.riediger
▴ 20
1
vote
1
reply
891
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 22 months ago by
Gordon Smyth
51k • written 22 months ago by
e.g.w.miller
▴ 10
1
vote
2
replies
1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
maria.soler
• 0
2
votes
1
reply
1.7k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 2.7 years ago by
Michael Love
42k • written 2.7 years ago by
BioNovice247
• 0
7
votes
12
replies
4.9k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 2.1 years ago by
Gordon Smyth
51k • written 8.6 years ago by
hamidrezarazzaghian
• 0
0
votes
2
replies
965
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR
DifferentialExpression
TMM
RNASeq
updated 2.7 years ago by
Gordon Smyth
51k • written 2.7 years ago by
hamidrezarazzaghian
• 0
3
votes
2
replies
902
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 4.2 years ago by
Rory Stark
★ 5.2k • written 4.2 years ago by
Guandong Shang
▴ 40
3
votes
1
reply
1.7k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.8 years ago
ATpoint
★ 4.2k
1
vote
1
reply
911
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma
TMM
differential expression
normalization
rnaseq
updated 5.2 years ago by
James W. MacDonald
66k • written 5.2 years ago by
natalia_lt
• 0
1
vote
4
replies
1.8k
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 5.5 years ago by
Gordon Smyth
51k • written 5.5 years ago by
rproendo
▴ 20
6
votes
7
replies
1.9k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 5.6 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 5.6 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 6.1 years ago by
Michael Love
42k • written 6.1 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 6.3 years ago by
Gordon Smyth
51k • written 6.3 years ago by
bilcodygm
• 0
3
votes
7
replies
5.9k
views
Limma PlotMDS: what values should be used?
limma
edger
plotmds
tmm
masigpro
6.5 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 7.1 years ago by
James W. MacDonald
66k • written 7.1 years ago by
jol.espinoz
▴ 40
2
votes
3
replies
2.6k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression
TMM
normalization
rnaseq
edger
7.2 years ago
aec
▴ 90
2
votes
7
replies
5.4k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
7.3 years ago
kkadzi25
• 0
0
votes
3
replies
2.0k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 7.4 years ago by
Rory Stark
★ 5.2k • written 7.4 years ago by
siklenkak
• 0
5
votes
4
replies
3.3k
views
Normalization factor in TMM method
TMM
normalization
edgeR
updated 7.7 years ago by
James W. MacDonald
66k • written 7.7 years ago by
Sara
▴ 10
0
votes
1
reply
1.9k
views
DiffBind TMM normalization
Rory Stark
diffbind
TMM
edgeR
chipseq
updated 8.0 years ago by
Rory Stark
★ 5.2k • written 8.1 years ago by
akdess
• 0
2
votes
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM
edgeR
8.0 years ago
humberto_munoz
• 0
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
8.0 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
3.3k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
saadmurtazakhan
▴ 10
4
votes
1
reply
4.7k
views
norm.factors in TMM normalisation
edgr
tmm
normalization
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 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
8.7 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 9.0 years ago by
Gordon Smyth
51k • written 9.0 years ago by
katherine.beaulieu14
• 0
28 results • Page
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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Stephanie M. Gogarten
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Jonathan
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