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tmm
•
reset
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
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
2
votes
7
replies
5.3k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
7.2 years ago
kkadzi25
• 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
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
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
7.9 years ago
saadmurtazakhan
▴ 10
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
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
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
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
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
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
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
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
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
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM
edgeR
7.9 years ago
humberto_munoz
• 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
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
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
5
votes
2
replies
684
views
PhD student
TMM
limma
10 months ago
Nisha
• 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
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
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
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
1
vote
1
reply
879
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
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
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
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
28 results • Page
1 of 1
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Replies
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…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
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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