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edaseq
•
reset
1
vote
4
replies
240
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
28 days ago • updated 27 days ago
samuel.channon
• 0
2
votes
2
replies
233
views
between lane normalization upper quantile
EDASeq
edgeR
4 weeks ago
elesofi
• 0
0
votes
1
reply
868
views
GC content
EDASeq
updated 22 months ago by
ATpoint
★ 4.0k • written 22 months ago by
Matilde
• 0
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
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
2
replies
932
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
3.4 years ago
gprezza
• 0
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
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
6
replies
1.0k
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
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
1
vote
1
reply
896
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
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
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
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
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
5.4 years ago
kbobowik
• 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
1
vote
1
reply
879
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
806
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
5.8 years ago
Dario Strbenac
★ 1.5k
2
votes
7
replies
23k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
5.9 years ago
zoppoli pietro
▴ 10
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
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
6
votes
11
replies
2.9k
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
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
llo
▴ 10
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
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
9
votes
7
replies
2.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
rahilsethi
• 0
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
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
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
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
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.0 years ago
Kasper Daniel Hansen
★ 6.5k
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
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
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
1.5k
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
35 results • Page
1 of 1
Recent ...
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by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Answer: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
You don't explain how many samples you have (columns of data), but the warning message shown in your post would arise if there are in fact …
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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