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Showing :
cpm
•
reset
5
votes
6
replies
294
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
7 weeks ago
mohammedtoufiq91
▴ 10
2
votes
7
replies
639
views
CPM after RUVseq
RUVSeq
CPM
Normalization
8 months ago
Jess
• 0
1
vote
1
reply
529
views
Degust: what normalization method does it use
DEGUST
Normalization
CPM
updated 16 months ago by
James W. MacDonald
62k • written 16 months ago by
Caroline
• 0
0
votes
2
replies
1.9k
views
CPM function in EDGER
edger
cpm
rnaseq
2.4 years ago
francesca3
• 0
0
votes
3
replies
367
views
Normalization of RNA seq data
RNA seq
cpm
updated 2.8 years ago by
Kevin Blighe
3.7k • written 2.8 years ago by
isabel.pieterse
• 0
3
votes
2
replies
387
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 2.9 years ago by
Rory Stark
★ 4.6k • written 2.9 years ago by
Guandong Shang
▴ 40
4
votes
5
replies
544
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
2.9 years ago
svlachavas
▴ 800
1
vote
2
replies
451
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 3.1 years ago by
Steve Lianoglou
13k • written 3.1 years ago by
zhang.jianhai
▴ 10
5
votes
7
replies
1.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
3.7 years ago
altintas.ali
• 0
3
votes
2
replies
612
views
How to calculate average log2 CPM with batch effect?
edger
limma
cpm
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
b.nota
▴ 360
2
votes
4
replies
781
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger
cpm
non-specific filtering
rnaseq
updated 4.5 years ago by
Gordon Smyth
47k • written 4.5 years ago by
svlachavas
▴ 800
15
votes
6
replies
21k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 4.6 years ago by
ftroot1010
▴ 20 • written 4.8 years ago by
jxb.dev
▴ 40
6
votes
14
replies
2.1k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis
variancestabilizingtransformation
normalization
cpm
edger
updated 4.7 years ago by
Wolfgang Huber
13k • written 4.7 years ago by
svlachavas
▴ 800
6
votes
2
replies
2.0k
views
edgeR cpm() function with and without log2
edger
cpm
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
b.nota
▴ 360
3
votes
8
replies
822
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
5.0 years ago
A
▴ 40
0
votes
3
replies
696
views
edgeR:fitted and partial expression values
edgeR
cpm
edger
fitted model
explained variance
updated 5.0 years ago by
Gordon Smyth
47k • written 5.0 years ago by
alakatos
▴ 120
4
votes
11
replies
3.2k
views
edgeR cpm filter
edger
independent filtering
multiple factor design
cpm
updated 5.3 years ago by
Gordon Smyth
47k • written 5.3 years ago by
teshome.dagnem
• 0
3
votes
9
replies
1.1k
views
edgeR long vectors support when normalizing abundance matrix
edger
cpm
5.3 years ago
jtremblay514
• 0
2
votes
7
replies
4.2k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
6.0 years ago
kkadzi25
• 0
1
vote
2
replies
1.6k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 6.4 years ago by
Gordon Smyth
47k • written 6.4 years ago by
lynski008
• 0
2
votes
7
replies
1.8k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 6.5 years ago by
Ryan C. Thompson
7.8k • written 6.5 years ago by
Sara
▴ 10
1
vote
6
replies
1.3k
views
extracting cpm expression from limma fit
limma
cpm
updated 6.6 years ago by
José Luis Lavín
▴ 10 • written 6.9 years ago by
map2085
▴ 40
1
vote
3
replies
1.8k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2
rnaseq
rna-seq
normalization
cpm
updated 6.7 years ago by
Wolfgang Huber
13k • written 6.7 years ago by
stwestreich
• 0
5
votes
4
replies
6.4k
views
edgeR cpm filter with >1 factor
edger
cpm
multiple factor design
independent filtering
7.0 years ago
dietahanson
▴ 30
11
votes
3
replies
2.7k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
7.1 years ago
mikaelhc
▴ 10
5
votes
3
replies
1.2k
views
Support for offsets in cpm and voom functions?
edgeR
cpm
voom
limma
7.3 years ago
Ryan C. Thompson
7.8k
0
votes
3
replies
3.0k
views
CPM output from edgeR for a downstream application
CPM
edgeR
7.7 years ago
ycding
▴ 10
27 results • Page
1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse
by
Eric
• 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Bernardo
• 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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