Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
TMM
•
reset
5
votes
2
replies
981
views
PhD student
TMM
limma
20 months ago
Nisha
• 0
1
vote
1
reply
1.1k
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
tleona3
• 0
1
vote
4
replies
1.6k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 2.5 years ago by
Simon Pearce
• 0 • written 2.5 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.2k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 2.6 years ago by
Gordon Smyth
52k • written 2.6 years ago by
e.g.w.miller
▴ 10
1
vote
2
replies
1.8k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 3.0 years ago by
maria.soler
• 0
2
votes
1
reply
2.3k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
BioNovice247
• 0
7
votes
12
replies
5.7k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 2.8 years ago by
Gordon Smyth
52k • written 9.3 years ago by
hamidrezarazzaghian
• 0
0
votes
2
replies
1.2k
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR
DifferentialExpression
TMM
RNASeq
updated 3.4 years ago by
Gordon Smyth
52k • written 3.4 years ago by
hamidrezarazzaghian
• 0
3
votes
2
replies
1.2k
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 5.0 years ago by
Rory Stark
★ 5.2k • written 5.0 years ago by
Guandong Shang
▴ 40
3
votes
1
reply
2.1k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
5.5 years ago
ATpoint
★ 4.7k
1
vote
1
reply
1.2k
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma
TMM
differential expression
normalization
rnaseq
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
natalia_lt
• 0
3
votes
4
replies
2.2k
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 6.2 years ago by
Gordon Smyth
52k • written 6.2 years ago by
rproendo
▴ 30
6
votes
7
replies
2.4k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 6.3 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 6.3 years ago by
Konstantinos Yeles
▴ 80
1
vote
4
replies
2.5k
views
processing of (salmon) gene counts for eqtl analysis
salmon
tximport
gene length
eqtl
TMM
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
VSM
▴ 120
0
votes
1
reply
1.4k
views
Limit on significant genes for TMM normalization
normalization
quantile normalization
tmm
edger
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
bilcodygm
• 0
3
votes
7
replies
6.8k
views
Limma PlotMDS: what values should be used?
limma
edger
plotmds
tmm
masigpro
7.2 years ago
dacaba.92
▴ 10
6
votes
4
replies
3.5k
views
Can edgeR TMM normalization be used for other count data?
edgeR
tmm
normalization
counts
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
jol.espinoz
▴ 40
2
votes
3
replies
2.9k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression
TMM
normalization
rnaseq
edger
7.9 years ago
aec
▴ 90
2
votes
7
replies
7.0k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
8.1 years ago
kkadzi25
• 0
0
votes
3
replies
2.3k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 8.1 years ago by
Rory Stark
★ 5.2k • written 8.2 years ago by
siklenkak
• 0
5
votes
4
replies
4.0k
views
Normalization factor in TMM method
TMM
normalization
edgeR
updated 8.4 years ago by
James W. MacDonald
68k • written 8.4 years ago by
Sara
▴ 20
0
votes
1
reply
2.3k
views
DiffBind TMM normalization
Rory Stark
diffbind
TMM
edgeR
chipseq
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.8 years ago by
akdess
• 0
2
votes
2
replies
1.6k
views
Sample sizes must be equal for TMM?
TMM
edgeR
8.7 years ago
humberto_munoz
• 0
5
votes
6
replies
2.4k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
8.8 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
3.9k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
saadmurtazakhan
▴ 10
4
votes
1
reply
5.2k
views
norm.factors in TMM normalisation
edgr
tmm
normalization
updated 9.4 years ago by
Aaron Lun
★ 28k • written 9.4 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
5
replies
12k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
9.4 years ago
nickbern92
• 0
4
votes
3
replies
3.1k
views
TMM Manual Calculation to be used in MATLAB on miRNA count data
matlab
calcnormfactors
TMM
edgeR
updated 9.8 years ago by
Gordon Smyth
52k • written 9.8 years ago by
katherine.beaulieu14
• 0
28 results • Page
1 of 1
Recent ...
Replies
Comment: sesameDataCache is not work properly on my system
by
Samreen
• 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data
by
James W. MacDonald
68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format
by
James W. MacDonald
68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages?
by
wilkinson
• 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification
by
ATpoint
★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
Awards
• All
Popular Question
to
Gordon Smyth
52k
Popular Question
to
AB
▴ 110
Popular Question
to
Lluís Revilla Sancho
▴ 760
Popular Question
to
tifaGis
• 0
Popular Question
to
Theo
▴ 10
Locations
• All
United States,
52 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
United States,
1 hour ago
The city by the bay,
2 hours ago
United States,
2 hours ago
Traffic: 675 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6