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edaseq
•
reset
0
votes
0
replies
255
views
Are equal whisker lengths important in an RLE plot?
EDASeq
EDA
3 months ago
BioinfGuru
▴ 70
2
votes
3
replies
496
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
3 months ago
BioinfGuru
▴ 70
1
vote
4
replies
642
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 months ago
samuel.channon
• 0
2
votes
2
replies
536
views
between lane normalization upper quantile
EDASeq
edgeR
8 months ago
elesofi
• 0
0
votes
1
reply
1.2k
views
GC content
EDASeq
updated 2.4 years ago by
ATpoint
★ 4.5k • written 2.4 years ago by
Matilde
• 0
2
votes
6
replies
1.5k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
3.5 years ago
Saulius
▴ 10
2
votes
2
replies
1.5k
views
EDASeq normalization: genes with 0 counts
edgeR
EDASeq
3.8 years ago • updated 3.5 years ago
gprezza
• 0
1
vote
2
replies
1.2k
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
4.0 years ago
gprezza
• 0
0
votes
0
replies
656
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
4.3 years ago
abf
▴ 30
1
vote
1
reply
1.7k
views
EDASeq gene length normalization
edaseq
r
rna-seq
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
karlaarz
• 0
1
vote
6
replies
1.3k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2
edaseq
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
vizio12341337
• 0
4
votes
7
replies
1.8k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 4.9 years ago by
Gordon Smyth
51k • written 4.9 years ago by
Ahdee
▴ 50
1
vote
1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
jeroen.gilis
▴ 90
0
votes
3
replies
1.2k
views
Possibly bug in newSeqExpressionSet function
software error
EDASeq
5.6 years ago
jens
• 0
1
vote
2
replies
1.5k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.9 years ago by
davide risso
▴ 980 • written 5.9 years ago by
Jon Bråte
▴ 260
2
votes
3
replies
2.1k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
maya.kappil
▴ 30
0
votes
0
replies
1.4k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
6.0 years ago
kbobowik
• 0
1
vote
9
replies
3.0k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 6.2 years ago by
davide risso
▴ 980 • written 6.2 years ago by
zoppoli pietro
▴ 10
1
vote
1
reply
1.1k
views
Mean-Variance Plot for Normalised Counts
EDASeq
meanVarPlot
updated 6.4 years ago by
davide risso
▴ 980 • written 6.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
941
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
6.4 years ago
Dario Strbenac
★ 1.5k
2
votes
7
replies
24k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
6.5 years ago
zoppoli pietro
▴ 10
0
votes
1
reply
1.9k
views
Incorporating 'offset' into edgeR pipeline
edgeR
EDASeq
offset
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
alakatos
▴ 130
2
votes
5
replies
2.7k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq
normalization
hg38
biomart
org.db
updated 7.0 years ago by
davide risso
▴ 980 • written 7.0 years ago by
mark.ebbert
• 0
6
votes
11
replies
3.5k
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 7.0 years ago by
antonio.colaprico
▴ 50 • written 7.0 years ago by
svlachavas
▴ 830
1
vote
1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 7.0 years ago by
davide risso
▴ 980 • written 7.0 years ago by
llo
▴ 10
1
vote
2
replies
1.8k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq
error
rna-seq
normalization
updated 8.4 years ago by
davide risso
▴ 980 • written 8.4 years ago by
reba.duncan
• 0
2
votes
2
replies
3.3k
views
How is the mean-variance plot calculated?
edaseq
updated 8.5 years ago by
Wolfgang Huber
★ 13k • written 8.5 years ago by
neverstop
• 0
9
votes
7
replies
3.3k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 9.2 years ago by
Gordon Smyth
51k • written 9.2 years ago by
rahilsethi
• 0
0
votes
4
replies
2.0k
views
False positives due to GC content correction - DESeq2
EDASeq
DESeq2
EDASeq
DESeq2
updated 10.3 years ago by
Michael Love
42k • written 10.3 years ago by
Guest User
★ 13k
2
votes
1
reply
2.1k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization
EDASeq
DESeq2
Normalization
EDASeq
DESeq2
updated 10.4 years ago by
Michael Love
42k • written 10.4 years ago by
Guest User
★ 13k
0
votes
3
replies
2.8k
views
EDASeq within normalization
Normalization
EDASeq
Normalization
EDASeq
updated 11.1 years ago by
davide risso
▴ 980 • written 11.1 years ago by
Catarina Almeida
▴ 30
0
votes
1
reply
1.4k
views
problem with aveLogCPM.default in edgeR
edgeR
EDASeq
edgeR
EDASeq
updated 11.5 years ago by
Gordon Smyth
51k • written 11.5 years ago by
suzy.stiegelmeyer@syngenta.com
▴ 40
0
votes
1
reply
2.1k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.6 years ago
Kasper Daniel Hansen
★ 6.5k
0
votes
1
reply
2.7k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 11.7 years ago by
Gordon Smyth
51k • written 11.7 years ago by
Ying W
▴ 90
0
votes
1
reply
1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn
EDASeq
cqn
EDASeq
updated 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.8 years ago by
Gordon Smyth
51k
0
votes
2
replies
2.1k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.8 years ago
love
▴ 150
0
votes
4
replies
1.7k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 12.8 years ago by
davide risso
▴ 980 • written 12.9 years ago by
rcaloger
▴ 500
37 results • Page
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Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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