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edaseq
•
reset
2
votes
7
replies
23k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
5.9 years ago
zoppoli pietro
▴ 10
2
votes
2
replies
3.0k
views
How is the mean-variance plot calculated?
edaseq
updated 7.9 years ago by
Wolfgang Huber
★ 13k • written 7.9 years ago by
neverstop
• 0
6
votes
11
replies
3.0k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks
rnaseq
normalization
EDASeq
updated 6.4 years ago by
antonio.colaprico
▴ 50 • written 6.4 years ago by
svlachavas
▴ 830
9
votes
7
replies
2.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
rahilsethi
• 0
1
vote
9
replies
2.6k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 5.6 years ago by
davide risso
▴ 950 • written 5.6 years ago by
zoppoli pietro
▴ 10
0
votes
3
replies
2.5k
views
EDASeq within normalization
Normalization
EDASeq
Normalization
EDASeq
updated 10.5 years ago by
davide risso
▴ 950 • written 10.5 years ago by
Catarina Almeida
▴ 30
0
votes
1
reply
2.5k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 11.1 years ago by
Gordon Smyth
50k • written 11.1 years ago by
Ying W
▴ 90
2
votes
5
replies
2.4k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq
normalization
hg38
biomart
org.db
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
mark.ebbert
• 0
2
votes
1
reply
1.9k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization
EDASeq
DESeq2
Normalization
EDASeq
DESeq2
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.1 years ago
Kasper Daniel Hansen
★ 6.5k
0
votes
2
replies
1.8k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.2 years ago
love
▴ 150
0
votes
4
replies
1.8k
views
False positives due to GC content correction - DESeq2
EDASeq
DESeq2
EDASeq
DESeq2
updated 9.7 years ago by
Michael Love
41k • written 9.7 years ago by
Guest User
★ 13k
2
votes
3
replies
1.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
maya.kappil
▴ 30
0
votes
1
reply
1.6k
views
Incorporating 'offset' into edgeR pipeline
edgeR
EDASeq
offset
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
alakatos
▴ 130
1
vote
2
replies
1.6k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq
error
rna-seq
normalization
updated 7.8 years ago by
davide risso
▴ 950 • written 7.8 years ago by
reba.duncan
• 0
4
votes
7
replies
1.5k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
Ahdee
▴ 50
0
votes
4
replies
1.5k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 12.2 years ago by
davide risso
▴ 950 • written 12.3 years ago by
rcaloger
▴ 500
0
votes
1
reply
1.5k
views
using offsets from EDASeq and cqn for edgeR
cqn
EDASeq
cqn
EDASeq
updated 11.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.2 years ago by
Gordon Smyth
50k
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
llo
▴ 10
1
vote
1
reply
1.4k
views
EDASeq gene length normalization
edaseq
r
rna-seq
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
karlaarz
• 0
1
vote
2
replies
1.3k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.3 years ago by
davide risso
▴ 950 • written 5.3 years ago by
Jon Bråte
▴ 250
0
votes
1
reply
1.3k
views
problem with aveLogCPM.default in edgeR
edgeR
EDASeq
edgeR
EDASeq
updated 10.9 years ago by
Gordon Smyth
50k • written 10.9 years ago by
suzy.stiegelmeyer@syngenta.com
▴ 40
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
2.9 years ago
Saulius
• 0
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
5.4 years ago
kbobowik
• 0
2
votes
2
replies
1.2k
views
EDASeq normalization: genes with 0 counts
edgeR
EDASeq
3.2 years ago • updated 2.9 years ago
gprezza
• 0
1
vote
6
replies
1.1k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2
edaseq
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
vizio12341337
• 0
0
votes
3
replies
1.0k
views
Possibly bug in newSeqExpressionSet function
software error
EDASeq
5.0 years ago
jens
• 0
1
vote
2
replies
933
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
3.4 years ago
gprezza
• 0
1
vote
1
reply
897
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
jeroen.gilis
▴ 90
1
vote
1
reply
881
views
Mean-Variance Plot for Normalised Counts
EDASeq
meanVarPlot
updated 5.8 years ago by
davide risso
▴ 950 • written 5.8 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
870
views
GC content
EDASeq
updated 22 months ago by
ATpoint
★ 4.0k • written 22 months ago by
Matilde
• 0
0
votes
1
reply
806
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
5.8 years ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
527
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
3.7 years ago
abf
▴ 30
1
vote
4
replies
251
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
4 weeks ago • updated 29 days ago
samuel.channon
• 0
2
votes
2
replies
236
views
between lane normalization upper quantile
EDASeq
edgeR
5 weeks ago • updated 4 weeks ago
elesofi
• 0
35 results • Page
1 of 1
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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