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Showing :
cqn
•
reset
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 12 months ago by
Michael Love
41k • written 12 months ago by
urwah
▴ 10
6
votes
9
replies
5.0k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
shankasal
• 0
0
votes
9
replies
2.1k
views
DESeq2 stuck running
cqn
DESeq2
cqn
DESeq2
updated 10.0 years ago by
Michael Love
41k • written 10.0 years ago by
Guest User
★ 13k
0
votes
9
replies
2.0k
views
normalization method & dispersion estimation RNA-seq data
Normalization
edgeR
cqn
Normalization
edgeR
cqn
updated 11.4 years ago by
Gordon Smyth
50k • written 11.4 years ago by
Guest User
★ 13k
0
votes
7
replies
2.2k
views
Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks
RNASeq
Annotation
Cancer
edgeR
cqn
easyRNASeq
RNASeq
Annotation
Cancer
edgeR
cqn
updated 11.4 years ago by
delhomme@embl.de
★ 1.2k • written 11.4 years ago by
Richard Friedman
★ 2.0k
0
votes
6
replies
2.2k
views
CQN to DEseq2
CQN
deseq2
updated 17 months ago by
Sally
• 0 • written 4.5 years ago by
nicholas.macknight
• 0
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
3.0 years ago
Saulius
• 0
0
votes
5
replies
3.7k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2
cqn
noiseq
updated 7.0 years ago by
Michael Love
41k • written 7.0 years ago by
glmazzo
▴ 10
0
votes
5
replies
3.1k
views
DESeq2
Normalization
Classification
Clustering
DESeq
cqn
DESeq2
Normalization
Classification
cqn
updated 11.1 years ago by
Michael Love
41k • written 11.2 years ago by
Wolfgang Huber
★ 13k
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
dmr210
▴ 30
3
votes
4
replies
4.2k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq
edgeR
cqn
RNASeq
edgeR
cqn
updated 10.1 years ago by
Martin Morgan
25k • written 10.1 years ago by
Matthew Thornton
▴ 350
1
vote
3
replies
1.2k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq
normalization
CQN
conditionalquartilenormalization
debugging
updated 5.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.2 years ago by
garbuzov
• 0
0
votes
3
replies
1.9k
views
Voom and CQN input
Normalization
limma
cqn
Normalization
limma
cqn
updated 10.4 years ago by
Gordon Smyth
50k • written 10.5 years ago by
Heather Estrella
▴ 30
4
votes
2
replies
1.3k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2
cqn
normalization
normalized counts
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
mark.ebbert
• 0
0
votes
2
replies
788
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization
R
cqn
17 months ago
Sally
• 0
4
votes
2
replies
2.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
s1437643
▴ 20
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
2
votes
2
replies
1.3k
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
6.0 years ago
shankasal
• 0
0
votes
1
reply
1.3k
views
CQN Package
RNASeq
cqn
RNASeq
cqn
updated 11.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.9 years ago by
Xin Davis
▴ 30
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.1 years ago
Kasper Daniel Hansen
★ 6.5k
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
1
vote
1
reply
1.2k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2
cqn
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
984366176
▴ 10
0
votes
1
reply
751
views
error using cqn package
Normalization
cqn
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
pegah.taklifi
▴ 30
0
votes
1
reply
1.2k
views
Error message running through CQN Vignette
Cancer
cqn
Cancer
cqn
updated 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.8 years ago by
Richard Friedman
★ 2.0k
1
vote
1
reply
873
views
CQN to DESeq2
cqn
DESeq2
updated 21 months ago by
Michael Love
41k • written 21 months ago by
bioinfo
• 0
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
2
votes
1
reply
1.4k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization
CQN
deseq2
RNA-seq
network
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
michael.pierrelee
• 0
0
votes
1
reply
1.1k
views
Conditional Quantile Normalization (cqn) error
cqn
normalization
conditionalquantilenormalization
atac-seq
updated 4.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 4.8 years ago by
Eric.Martin
• 0
0
votes
1
reply
1.3k
views
CQN normalization
cqn
cqn
updated 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.8 years ago by
Sermsawat Tunlaya-anukit
▴ 90
0
votes
1
reply
953
views
Is CQN compatible with DESeq2?
deseq2
cqn
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
nicholas.macknight
• 0
0
votes
0
replies
912
views
package announcement: cqn
Normalization
cqn
Normalization
cqn
12.8 years ago
Kasper Daniel Hansen
★ 6.5k
0
votes
0
replies
1.1k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn
sqn
8.3 years ago
s1437643
▴ 20
0
votes
0
replies
656
views
CQN Normalization not removing bias
cqn
4.4 years ago
nicholas.macknight
• 0
0
votes
0
replies
713
views
cqn vignette error
cqn
normalization
edger
4.4 years ago
Jenny Drnevich
★ 2.0k
34 results • Page
1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Awards
• All
Scholar
to
Michael Love
41k
Popular Question
to
Malcolm Cook
★ 1.6k
Teacher
to
Gordon Smyth
50k
Popular Question
to
priyanka.m
• 0
Popular Question
to
Vincent J. Carey, Jr.
6.7k
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