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EDAseq
•
reset
0
votes
0
replies
462
views
Are equal whisker lengths important in an RLE plot?
EDASeq
EDA
14 months ago
BioinfGuru
▴ 70
2
votes
3
replies
1.2k
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
14 months ago
BioinfGuru
▴ 70
1
vote
4
replies
1.1k
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
19 months ago
samuel.channon
• 0
2
votes
2
replies
894
views
between lane normalization upper quantile
EDASeq
edgeR
19 months ago
elesofi
• 0
0
votes
1
reply
1.5k
views
GC content
EDASeq
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Matilde
• 0
2
votes
6
replies
1.9k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
4.5 years ago
Saulius
▴ 10
2
votes
2
replies
1.9k
views
EDASeq normalization: genes with 0 counts
edgeR
EDASeq
4.7 years ago • updated 4.4 years ago
gprezza
• 0
1
vote
2
replies
1.5k
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
4.9 years ago
gprezza
• 0
0
votes
0
replies
818
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
5.2 years ago
abf
▴ 30
1
vote
1
reply
2.2k
views
EDASeq gene length normalization
edaseq
r
rna-seq
updated 5.5 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
karlaarz
• 0
1
vote
6
replies
1.6k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2
edaseq
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
vizio12341337
• 0
4
votes
7
replies
2.3k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 5.8 years ago by
Gordon Smyth
53k • written 5.9 years ago by
Ahdee
▴ 60
1
vote
1
reply
1.2k
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
jeroen.gilis
▴ 100
0
votes
3
replies
1.5k
views
Possibly bug in newSeqExpressionSet function
software error
EDASeq
6.5 years ago
jens
• 0
1
vote
2
replies
1.7k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.8 years ago by
davide risso
▴ 980 • written 6.8 years ago by
Jon Bråte
▴ 270
2
votes
3
replies
2.6k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
maya.kappil
▴ 30
0
votes
0
replies
1.7k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
6.9 years ago
kbobowik
• 0
1
vote
9
replies
3.5k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 7.1 years ago by
davide risso
▴ 980 • written 7.1 years ago by
zoppoli pietro
▴ 10
1
vote
1
reply
1.4k
views
Mean-Variance Plot for Normalised Counts
EDASeq
meanVarPlot
updated 7.4 years ago by
davide risso
▴ 980 • written 7.4 years ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
1.1k
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
7.4 years ago
Dario Strbenac
★ 1.6k
2
votes
7
replies
26k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
7.5 years ago
zoppoli pietro
▴ 10
0
votes
1
reply
2.2k
views
Incorporating 'offset' into edgeR pipeline
edgeR
EDASeq
offset
updated 7.8 years ago by
Aaron Lun
★ 29k • written 7.8 years ago by
alakatos
▴ 130
2
votes
5
replies
3.1k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq
normalization
hg38
biomart
org.db
updated 7.9 years ago by
davide risso
▴ 980 • written 7.9 years ago by
mark.ebbert
• 0
6
votes
11
replies
4.2k
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 7.9 years ago by
antonio.colaprico
▴ 50 • written 7.9 years ago by
svlachavas
▴ 840
1
vote
1
reply
2.0k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 8.0 years ago by
davide risso
▴ 980 • written 8.0 years ago by
llo
▴ 10
1
vote
2
replies
2.0k
views
Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq
error
rna-seq
normalization
updated 9.4 years ago by
davide risso
▴ 980 • written 9.4 years ago by
reba.duncan
• 0
2
votes
2
replies
3.7k
views
How is the mean-variance plot calculated?
edaseq
updated 9.4 years ago by
Wolfgang Huber
★ 13k • written 9.4 years ago by
neverstop
• 0
9
votes
7
replies
3.9k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 10.2 years ago by
Gordon Smyth
53k • written 10.2 years ago by
rahilsethi
• 0
0
votes
4
replies
2.3k
views
False positives due to GC content correction - DESeq2
EDASeq
DESeq2
EDASeq
DESeq2
updated 11.2 years ago by
Michael Love
43k • written 11.2 years ago by
Guest User
★ 13k
2
votes
1
reply
2.2k
views
DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Normalization
EDASeq
DESeq2
Normalization
EDASeq
DESeq2
updated 11.3 years ago by
Michael Love
43k • written 11.3 years ago by
Guest User
★ 13k
0
votes
3
replies
3.1k
views
EDASeq within normalization
Normalization
EDASeq
Normalization
EDASeq
updated 12.0 years ago by
davide risso
▴ 980 • written 12.0 years ago by
Catarina Almeida
▴ 30
0
votes
1
reply
1.6k
views
problem with aveLogCPM.default in edgeR
edgeR
EDASeq
edgeR
EDASeq
updated 12.4 years ago by
Gordon Smyth
53k • written 12.4 years ago by
suzy.stiegelmeyer@syngenta.com
▴ 40
0
votes
1
reply
2.3k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
12.6 years ago
Kasper Daniel Hansen
★ 6.5k
0
votes
1
reply
3.0k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 12.6 years ago by
Gordon Smyth
53k • written 12.6 years ago by
Ying W
▴ 90
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
cqn
EDASeq
cqn
EDASeq
updated 12.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.7 years ago by
Gordon Smyth
53k
0
votes
2
replies
2.4k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
12.7 years ago
love
▴ 150
0
votes
4
replies
2.0k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 13.7 years ago by
davide risso
▴ 980 • written 13.8 years ago by
rcaloger
▴ 500
37 results • Page
1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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