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tmm
•
reset
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.5 years ago
nickbern92
• 0
3
votes
7
replies
5.6k
views
Limma PlotMDS: what values should be used?
limma
edger
plotmds
tmm
masigpro
6.3 years ago
dacaba.92
▴ 10
2
votes
7
replies
5.2k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
7.1 years ago
kkadzi25
• 0
7
votes
12
replies
4.6k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 22 months ago by
Gordon Smyth
50k • written 8.4 years ago by
hamidrezarazzaghian
• 0
4
votes
1
reply
4.6k
views
norm.factors in TMM normalisation
edgr
tmm
normalization
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
Assa Yeroslaviz
★ 1.5k
6
votes
4
replies
3.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR
tmm
normalization
counts
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
jol.espinoz
▴ 40
1
vote
18
replies
3.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
saadmurtazakhan
▴ 10
5
votes
4
replies
3.1k
views
Normalization factor in TMM method
TMM
normalization
edgeR
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
Sara
▴ 10
4
votes
3
replies
2.8k
views
TMM Manual Calculation to be used in MATLAB on miRNA count data
matlab
calcnormfactors
TMM
edgeR
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
katherine.beaulieu14
• 0
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
7.0 years ago
aec
▴ 90
1
vote
4
replies
2.0k
views
processing of (salmon) gene counts for eqtl analysis
salmon
tximport
gene length
eqtl
TMM
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
VSM
▴ 120
5
votes
6
replies
1.9k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
7.8 years ago
saadmurtazakhan
▴ 10
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 7.2 years ago by
Rory Stark
★ 5.1k • written 7.2 years ago by
siklenkak
• 0
0
votes
1
reply
1.8k
views
DiffBind TMM normalization
Rory Stark
diffbind
TMM
edgeR
chipseq
updated 7.7 years ago by
Rory Stark
★ 5.1k • written 7.9 years ago by
akdess
• 0
6
votes
7
replies
1.8k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 5.3 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 5.3 years ago by
Konstantinos Yeles
▴ 80
1
vote
4
replies
1.6k
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
rproendo
▴ 20
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.6 years ago
ATpoint
★ 4.0k
2
votes
1
reply
1.5k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
BioNovice247
• 0
2
votes
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM
edgeR
7.8 years ago
humberto_munoz
• 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.0 years ago by
Rory Stark
★ 5.1k • written 2.0 years ago by
maria.soler
• 0
0
votes
1
reply
1.0k
views
Limit on significant genes for TMM normalization
normalization
quantile normalization
tmm
edger
updated 6.1 years ago by
Gordon Smyth
50k • written 6.1 years ago by
bilcodygm
• 0
1
vote
4
replies
1.0k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 18 months ago by
Simon Pearce
• 0 • written 18 months ago by
a.riediger
▴ 20
0
votes
2
replies
914
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR
DifferentialExpression
TMM
RNASeq
updated 2.5 years ago by
Gordon Smyth
50k • written 2.5 years ago by
hamidrezarazzaghian
• 0
1
vote
1
reply
851
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma
TMM
differential expression
normalization
rnaseq
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
natalia_lt
• 0
3
votes
2
replies
823
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 4.0 years ago by
Rory Stark
★ 5.1k • written 4.0 years ago by
Guandong Shang
▴ 40
1
vote
1
reply
782
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 20 months ago by
Gordon Smyth
50k • written 20 months ago by
e.g.w.miller
▴ 10
1
vote
1
reply
689
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
tleona3
• 0
5
votes
2
replies
637
views
PhD student
TMM
limma
8 months ago
Nisha
• 0
28 results • Page
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Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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