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Showing :
cqn
•
reset
3
votes
12
replies
1.3k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 11 months ago by
Michael Love
41k • written 11 months ago by
urwah
▴ 10
0
votes
2
replies
718
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
16 months ago
Sally
• 0
1
vote
1
reply
831
views
CQN to DESeq2
cqn
DESeq2
updated 19 months ago by
Michael Love
41k • written 20 months ago by
bioinfo
• 0
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2
cqn
EDASeq
2.9 years ago
Saulius
• 0
0
votes
1
reply
702
views
error using cqn package
Normalization
cqn
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
pegah.taklifi
▴ 30
0
votes
0
replies
688
views
cqn vignette error
cqn
normalization
edger
4.3 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
620
views
CQN Normalization not removing bias
cqn
4.3 years ago
nicholas.macknight
• 0
0
votes
6
replies
2.1k
views
CQN to DEseq2
CQN
deseq2
updated 15 months ago by
Sally
• 0 • written 4.3 years ago by
nicholas.macknight
• 0
0
votes
1
reply
915
views
Is CQN compatible with DESeq2?
deseq2
cqn
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
nicholas.macknight
• 0
0
votes
1
reply
1.0k
views
Conditional Quantile Normalization (cqn) error
cqn
normalization
conditionalquantilenormalization
atac-seq
updated 4.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 4.7 years ago by
Eric.Martin
• 0
2
votes
1
reply
1.4k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization
CQN
deseq2
RNA-seq
network
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
michael.pierrelee
• 0
1
vote
3
replies
1.1k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq
normalization
CQN
conditionalquartilenormalization
debugging
updated 5.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.0 years ago by
garbuzov
• 0
2
votes
2
replies
1.2k
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
5.9 years ago
shankasal
• 0
6
votes
9
replies
4.8k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
shankasal
• 0
4
votes
2
replies
1.2k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2
cqn
normalization
normalized counts
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
mark.ebbert
• 0
1
vote
1
reply
1.2k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2
cqn
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
984366176
▴ 10
0
votes
5
replies
3.6k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2
cqn
noiseq
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
glmazzo
▴ 10
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 7.0 years ago by
Michael Love
41k • written 7.0 years ago by
dmr210
▴ 30
4
votes
2
replies
2.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
s1437643
▴ 20
0
votes
0
replies
1.1k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn
sqn
8.2 years ago
s1437643
▴ 20
0
votes
9
replies
2.0k
views
DESeq2 stuck running
cqn
DESeq2
cqn
DESeq2
updated 9.9 years ago by
Michael Love
41k • written 9.9 years ago by
Guest User
★ 13k
3
votes
4
replies
4.1k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq
edgeR
cqn
RNASeq
edgeR
cqn
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
Matthew Thornton
▴ 350
0
votes
3
replies
1.8k
views
Voom and CQN input
Normalization
limma
cqn
Normalization
limma
cqn
updated 10.3 years ago by
Gordon Smyth
50k • written 10.3 years ago by
Heather Estrella
▴ 30
0
votes
1
reply
1.8k
views
using offsets from EDASeq and cqn for edgeR
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.0 years ago
Kasper Daniel Hansen
★ 6.5k
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 11.0 years ago by
Gordon Smyth
50k • written 11.0 years ago by
Ying W
▴ 90
0
votes
5
replies
3.1k
views
DESeq2
Normalization
Classification
Clustering
DESeq
cqn
DESeq2
Normalization
Classification
cqn
updated 11.0 years ago by
Michael Love
41k • written 11.0 years ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
1.5k
views
using offsets from EDASeq and cqn for edgeR
cqn
EDASeq
cqn
EDASeq
updated 11.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.1 years ago by
Gordon Smyth
50k
0
votes
2
replies
1.8k
views
using offsets from EDASeq and cqn
GO
edgeR
cqn
EDASeq
GO
edgeR
cqn
EDASeq
11.1 years ago
love
▴ 150
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 11.3 years ago by
delhomme@embl.de
★ 1.2k • written 11.3 years ago by
Richard Friedman
★ 2.0k
0
votes
9
replies
2.0k
views
normalization method & dispersion estimation RNA-seq data
Normalization
edgeR
cqn
Normalization
edgeR
cqn
updated 11.3 years ago by
Gordon Smyth
50k • written 11.3 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
CQN normalization
cqn
cqn
updated 11.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.7 years ago by
Sermsawat Tunlaya-anukit
▴ 90
0
votes
1
reply
1.1k
views
Error message running through CQN Vignette
Cancer
cqn
Cancer
cqn
updated 11.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.7 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
1.3k
views
CQN Package
RNASeq
cqn
RNASeq
cqn
updated 11.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.7 years ago by
Xin Davis
▴ 30
0
votes
0
replies
891
views
package announcement: cqn
Normalization
cqn
Normalization
cqn
12.7 years ago
Kasper Daniel Hansen
★ 6.5k
34 results • Page
1 of 1
Recent ...
Replies
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
Awards
• All
Scholar
to
James W. MacDonald
65k
Scholar
to
Gordon Smyth
50k
Popular Question
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rocanja
▴ 60
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rproendo
▴ 20
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Wolfgang RAFFELSBERGER
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