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Showing :
CQN
•
reset
2
votes
4
replies
681
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
written 4 months ago by
emlucero
• 0
3
votes
12
replies
2.0k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 19 months ago by
Michael Love
43k • written 19 months ago by
urwah
▴ 10
0
votes
2
replies
1.0k
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
2.0 years ago
Sally
• 0
1
vote
1
reply
1.1k
views
CQN to DESeq2
cqn
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
bioinfo
• 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
0
votes
1
reply
910
views
error using cqn package
Normalization
cqn
updated 4.0 years ago by
James W. MacDonald
67k • written 4.0 years ago by
pegah.taklifi
▴ 30
0
votes
0
replies
863
views
cqn vignette error
cqn
normalization
edger
5.0 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
784
views
CQN Normalization not removing bias
cqn
5.0 years ago
nicholas.macknight
• 0
0
votes
6
replies
2.5k
views
CQN to DEseq2
CQN
deseq2
updated 24 months ago by
Sally
• 0 • written 5.0 years ago by
nicholas.macknight
• 0
0
votes
1
reply
1.2k
views
Is CQN compatible with DESeq2?
deseq2
cqn
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
nicholas.macknight
• 0
0
votes
1
reply
1.3k
views
Conditional Quantile Normalization (cqn) error
cqn
normalization
conditionalquantilenormalization
atac-seq
updated 5.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.4 years ago by
Eric.Martin
• 0
2
votes
1
reply
1.7k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization
CQN
deseq2
RNA-seq
network
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
michael.pierrelee
• 0
1
vote
3
replies
1.4k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq
normalization
CQN
conditionalquartilenormalization
debugging
updated 5.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.7 years ago by
garbuzov
• 0
2
votes
2
replies
1.5k
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
6.5 years ago
shankasal
• 0
6
votes
9
replies
5.8k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
shankasal
• 0
4
votes
2
replies
1.5k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2
cqn
normalization
normalized counts
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
mark.ebbert
• 0
1
vote
1
reply
1.4k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2
cqn
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
984366176
▴ 10
0
votes
5
replies
4.1k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2
cqn
noiseq
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
glmazzo
▴ 10
9
votes
4
replies
3.7k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
dmr210
▴ 30
4
votes
2
replies
2.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
s1437643
▴ 20
0
votes
0
replies
1.2k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn
sqn
8.9 years ago
s1437643
▴ 20
0
votes
9
replies
2.2k
views
DESeq2 stuck running
cqn
DESeq2
cqn
DESeq2
updated 10.5 years ago by
Michael Love
43k • written 10.6 years ago by
Guest User
★ 13k
3
votes
4
replies
4.5k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq
edgeR
cqn
RNASeq
edgeR
cqn
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
Matthew Thornton
▴ 380
0
votes
3
replies
2.0k
views
Voom and CQN input
Normalization
limma
cqn
Normalization
limma
cqn
updated 11.0 years ago by
Gordon Smyth
51k • written 11.0 years ago by
Heather Estrella
▴ 30
0
votes
1
reply
2.1k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.7 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
5
replies
3.4k
views
DESeq2
Normalization
Classification
Clustering
DESeq
cqn
DESeq2
Normalization
Classification
cqn
updated 11.7 years ago by
Michael Love
43k • written 11.7 years ago by
Wolfgang Huber
★ 13k
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
7
replies
2.5k
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 12.0 years ago by
delhomme@embl.de
★ 1.2k • written 12.0 years ago by
Richard Friedman
★ 2.0k
0
votes
9
replies
2.3k
views
normalization method & dispersion estimation RNA-seq data
Normalization
edgeR
cqn
Normalization
edgeR
cqn
updated 12.0 years ago by
Gordon Smyth
51k • written 12.0 years ago by
Guest User
★ 13k
0
votes
1
reply
1.5k
views
CQN normalization
cqn
cqn
updated 12.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.4 years ago by
Sermsawat Tunlaya-anukit
▴ 90
0
votes
1
reply
1.3k
views
Error message running through CQN Vignette
Cancer
cqn
Cancer
cqn
updated 12.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.4 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
1.5k
views
CQN Package
RNASeq
cqn
RNASeq
cqn
updated 12.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.4 years ago by
Xin Davis
▴ 30
0
votes
0
replies
1.0k
views
package announcement: cqn
Normalization
cqn
Normalization
cqn
13.4 years ago
Kasper Daniel Hansen
★ 6.5k
35 results • Page
1 of 1
Recent ...
Replies
Answer: Epic v2 Annotation CpG_maf source?
by
James W. MacDonald
67k
Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…
Comment: Deseq2 res Function
by
James W. MacDonald
67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data
by
James W. MacDonald
67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Robert Castelo
★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Votes
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
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