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Showing :
EDASeq
•
reset
2
votes
6
replies
462
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
12 months ago
Saulius
• 0
2
votes
2
replies
343
views
EDASeq normalization: genes with 0 counts
edgeR
EDASeq
15 months ago • updated 11 months ago
gprezza
• 0
1
vote
2
replies
387
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
18 months ago • updated 17 months ago
gprezza
• 0
0
votes
0
replies
249
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
22 months ago
abf
▴ 30
1
vote
1
reply
608
views
EDASeq gene length normalization
edaseq
r
rna-seq
updated 2.1 years ago by
Kevin Blighe
3.5k • written 2.1 years ago by
karlaarz
• 0
1
vote
6
replies
474
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2
edaseq
updated 2.4 years ago by
Michael Love
36k • written 2.4 years ago by
vizio12341337
• 0
4
votes
7
replies
646
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 2.4 years ago by
Gordon Smyth
45k • written 2.4 years ago by
Ahdee
▴ 50
1
vote
1
reply
364
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 2.8 years ago by
Michael Love
36k • written 2.8 years ago by
jeroen.gilis
▴ 30
0
votes
3
replies
485
views
Possibly bug in newSeqExpressionSet function
software error
EDASeq
3.1 years ago
jens
• 0
1
vote
2
replies
667
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 3.3 years ago by
davide risso
▴ 890 • written 3.3 years ago by
Jon Bråte
▴ 180
2
votes
3
replies
850
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 3.5 years ago by
Michael Love
36k • written 3.5 years ago by
maya.kappil
▴ 20
0
votes
0
replies
570
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
3.5 years ago
kbobowik
• 0
1
vote
9
replies
1.4k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 3.6 years ago by
davide risso
▴ 890 • written 3.6 years ago by
zoppoli pietro
▴ 10
1
vote
1
reply
436
views
Mean-Variance Plot for Normalised Counts
EDASeq
meanVarPlot
updated 3.9 years ago by
davide risso
▴ 890 • written 3.9 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
443
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
3.9 years ago
Dario Strbenac
★ 1.5k
2
votes
7
replies
12k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
4.0 years ago
zoppoli pietro
▴ 10
0
votes
1
reply
931
views
Incorporating 'offset' into edgeR pipeline
edgeR
EDASeq
offset
updated 4.3 years ago by
Aaron Lun
★ 27k • written 4.3 years ago by
alakatos
▴ 120
2
votes
5
replies
1.3k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq
normalization
hg38
biomart
org.db
updated 4.5 years ago by
davide risso
▴ 890 • written 4.5 years ago by
mark.ebbert
• 0
6
votes
11
replies
1.7k
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 4.5 years ago by
antonio.colaprico
▴ 40 • written 4.5 years ago by
svlachavas
▴ 780
1
vote
1
reply
858
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 4.5 years ago by
davide risso
▴ 890 • written 4.5 years ago by
llo
▴ 10
1
vote
2
replies
1000
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq
error
rna-seq
normalization
updated 5.9 years ago by
davide risso
▴ 890 • written 5.9 years ago by
reba.duncan
• 0
2
votes
2
replies
2.0k
views
How is the mean-variance plot calculated?
edaseq
updated 6.0 years ago by
Wolfgang Huber
13k • written 6.0 years ago by
neverstop
• 0
9
votes
7
replies
1.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 6.7 years ago by
Gordon Smyth
45k • written 6.7 years ago by
rahilsethi
• 0
0
votes
4
replies
1.3k
views
False positives due to GC content correction - DESeq2
EDASeq
DESeq2
EDASeq
DESeq2
updated 7.8 years ago by
Michael Love
36k • written 7.8 years ago by
Guest User
★ 12k
2
votes
1
reply
1.6k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization
EDASeq
DESeq2
Normalization
EDASeq
DESeq2
updated 7.9 years ago by
Michael Love
36k • written 7.9 years ago by
Guest User
★ 12k
0
votes
3
replies
1.9k
views
EDASeq within normalization
Normalization
EDASeq
Normalization
EDASeq
updated 8.6 years ago by
davide risso
▴ 890 • written 8.6 years ago by
Catarina Almeida
▴ 30
0
votes
1
reply
862
views
problem with aveLogCPM.default in edgeR
edgeR
EDASeq
edgeR
EDASeq
updated 9.0 years ago by
Gordon Smyth
45k • written 9.0 years ago by
suzy.stiegelmeyer@syngenta.com
▴ 40
0
votes
1
reply
1.4k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
9.1 years ago
Kasper Daniel Hansen
6.5k
0
votes
1
reply
2.0k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 9.2 years ago by
Gordon Smyth
45k • written 9.2 years ago by
Ying W
▴ 90
0
votes
1
reply
985
views
using offsets from EDASeq and cqn for edgeR
cqn
EDASeq
cqn
EDASeq
updated 9.2 years ago by
Kasper Daniel Hansen
6.5k • written 9.2 years ago by
Gordon Smyth
45k
0
votes
2
replies
1.3k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
9.3 years ago
love
▴ 150
0
votes
4
replies
973
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 10.3 years ago by
davide risso
▴ 890 • written 10.4 years ago by
rcaloger
▴ 500
32 results • Page
1 of 1
Recent ...
Replies
Answer: how to make a group to apply the data to CAMERA
by
Gordon Smyth
45k
See the [limma User's Guide](https://www.bioconductor.org/packages/3.15/bioc/vignettes/limma/inst/doc/usersguide.pdf) for how to undertake …
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Guido Hooiveld
★ 3.2k
To add to the extensive discussion above, you may also want to have a look at the so-called UPC algorithm, available in the [package][1] `S…
Answer: How to best visualize multi-level transcriptomics experiment data?
by
Gordon Smyth
45k
> One way is to extract the differentially expressed genes with p.val = 0.05 and logFC = +/-1.0 I strongly recommend using FDR < 0.05 and…
Comment: Reading multiple data segments from FCS 3.0 file
by
Goldpanda
• 0
Is there a way to combine the fcs files back into a single file as individual data segments?
Answer: different results in DESeq2 when comparing groups in two ways
by
zohreh.fazelan
• 0
I appreciate your time and response.
Votes
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
A: coefficient not estimable (limma warning)
A: conceptual question about FDR, FDR adjusted p-value and q-value
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