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EDAseq
•
reset
0
votes
0
replies
308
views
Are equal whisker lengths important in an RLE plot?
EDASeq
EDA
6 months ago
BioinfGuru
▴ 70
2
votes
3
replies
675
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
6 months ago
BioinfGuru
▴ 70
1
vote
4
replies
759
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
11 months ago • updated 10 months ago
samuel.channon
• 0
2
votes
2
replies
628
views
between lane normalization upper quantile
EDASeq
edgeR
11 months ago
elesofi
• 0
0
votes
1
reply
1.3k
views
GC content
EDASeq
updated 2.6 years ago by
ATpoint
★ 4.7k • written 2.6 years ago by
Matilde
• 0
2
votes
6
replies
1.6k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
3.8 years ago
Saulius
▴ 10
2
votes
2
replies
1.6k
views
EDASeq normalization: genes with 0 counts
edgeR
EDASeq
4.0 years ago • updated 3.7 years ago
gprezza
• 0
1
vote
2
replies
1.3k
views
Roast (fry) gene set testing with offset
EDASeq
edgeR
limma
4.2 years ago
gprezza
• 0
0
votes
0
replies
694
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
4.5 years ago
abf
▴ 30
1
vote
1
reply
1.8k
views
EDASeq gene length normalization
edaseq
r
rna-seq
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 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 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
vizio12341337
• 0
4
votes
7
replies
1.9k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma
voom
edaseq
edger
rnaseq
updated 5.2 years ago by
Gordon Smyth
52k • written 5.2 years ago by
Ahdee
▴ 50
1
vote
1
reply
1.1k
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
jeroen.gilis
▴ 90
0
votes
3
replies
1.3k
views
Possibly bug in newSeqExpressionSet function
software error
EDASeq
5.9 years ago
jens
• 0
1
vote
2
replies
1.6k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 6.1 years ago by
davide risso
▴ 980 • written 6.1 years ago by
Jon Bråte
▴ 260
2
votes
3
replies
2.3k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
maya.kappil
▴ 30
0
votes
0
replies
1.5k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
6.2 years ago
kbobowik
• 0
1
vote
9
replies
3.1k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 6.4 years ago by
davide risso
▴ 980 • written 6.4 years ago by
zoppoli pietro
▴ 10
1
vote
1
reply
1.2k
views
Mean-Variance Plot for Normalised Counts
EDASeq
meanVarPlot
updated 6.7 years ago by
davide risso
▴ 980 • written 6.7 years ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
978
views
meanVarPlot Ignores Sample Total Count Differences
EDASeq
meanVarPlot
6.7 years ago
Dario Strbenac
★ 1.6k
2
votes
7
replies
25k
views
use EDAseq normalized data as input of DESeq2
deseq2
edaseq
6.8 years ago
zoppoli pietro
▴ 10
0
votes
1
reply
2.0k
views
Incorporating 'offset' into edgeR pipeline
edgeR
EDASeq
offset
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
alakatos
▴ 130
2
votes
5
replies
2.9k
views
getGeneLengthAndGCContent: "zero or more than one input sequence"
edaseq
normalization
hg38
biomart
org.db
updated 7.2 years ago by
davide risso
▴ 980 • written 7.2 years ago by
mark.ebbert
• 0
6
votes
11
replies
3.7k
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 7.2 years ago by
antonio.colaprico
▴ 50 • written 7.2 years ago by
svlachavas
▴ 840
1
vote
1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 7.3 years ago by
davide risso
▴ 980 • written 7.3 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 8.7 years ago by
davide risso
▴ 980 • written 8.7 years ago by
reba.duncan
• 0
2
votes
2
replies
3.4k
views
How is the mean-variance plot calculated?
edaseq
updated 8.8 years ago by
Wolfgang Huber
★ 13k • written 8.8 years ago by
neverstop
• 0
9
votes
7
replies
3.5k
views
How to use normalized values by EDASeq in edgeR?
edgeR
EDASeq
updated 9.5 years ago by
Gordon Smyth
52k • written 9.5 years ago by
rahilsethi
• 0
0
votes
4
replies
2.1k
views
False positives due to GC content correction - DESeq2
EDASeq
DESeq2
EDASeq
DESeq2
updated 10.5 years ago by
Michael Love
43k • written 10.5 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 10.6 years ago by
Michael Love
43k • written 10.6 years ago by
Guest User
★ 13k
0
votes
3
replies
2.9k
views
EDASeq within normalization
Normalization
EDASeq
Normalization
EDASeq
updated 11.3 years ago by
davide risso
▴ 980 • written 11.4 years ago by
Catarina Almeida
▴ 30
0
votes
1
reply
1.5k
views
problem with aveLogCPM.default in edgeR
edgeR
EDASeq
edgeR
EDASeq
updated 11.7 years ago by
Gordon Smyth
52k • written 11.8 years ago by
suzy.stiegelmeyer@syngenta.com
▴ 40
0
votes
1
reply
2.2k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.9 years ago
Kasper Daniel Hansen
★ 6.5k
0
votes
1
reply
2.8k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 11.9 years ago by
Gordon Smyth
52k • written 11.9 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 12.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.0 years ago by
Gordon Smyth
52k
0
votes
2
replies
2.1k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
12.0 years ago
love
▴ 150
0
votes
4
replies
1.8k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 13.1 years ago by
davide risso
▴ 980 • written 13.1 years ago by
rcaloger
▴ 500
37 results • Page
1 of 1
Recent ...
Replies
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction
by
bbao
▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Votes
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
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