Showing : CQN • reset
2
votes
4
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1.2k
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 17 months ago by • 0
3
votes
12
replies
2.9k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.3k
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
3.0 years ago Sally • 0
1
vote
1
reply
1.3k
views
CQN to DESeq2
cqn DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
2
votes
6
replies
2.0k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.6 years ago Saulius ▴ 10
0
votes
1
reply
1.2k
views
error using cqn package
Normalization cqn
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 30
0
votes
0
replies
1.0k
views
cqn vignette error
cqn normalization edger
6.0 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.1k
views
CQN Normalization not removing bias
cqn
6.0 years ago nicholas.macknight • 0
0
votes
6
replies
3.0k
views
CQN to DEseq2
CQN deseq2
updated 3.0 years ago by • 0 • written 6.0 years ago by • 0
0
votes
1
reply
1.5k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.6k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 6.4 years ago by ★ 6.5k • written 6.4 years ago by • 0
2
votes
1
reply
2.1k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
3
replies
1.7k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 6.7 years ago by ★ 6.5k • written 6.7 years ago by • 0
2
votes
2
replies
1.9k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
7.6 years ago shankasal • 0
6
votes
9
replies
7.2k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
4
votes
2
replies
1.7k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2 cqn normalization normalized counts
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
1
vote
1
reply
1.6k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2 cqn
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
0
votes
5
replies
4.8k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
9
votes
4
replies
4.4k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
4
votes
2
replies
3.0k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 20
0
votes
0
replies
1.4k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
9.9 years ago s1437643 ▴ 20
0
votes
9
replies
2.6k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 11.6 years ago by 43k • written 11.6 years ago by ★ 13k
3
votes
4
replies
4.9k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 11.7 years ago by 25k • written 11.7 years ago by ▴ 390
0
votes
3
replies
2.3k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 30
0
votes
1
reply
2.4k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.7 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 12.7 years ago by 53k • written 12.7 years ago by ▴ 90
0
votes
5
replies
3.9k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 12.7 years ago by 43k • written 12.7 years ago by ★ 13k
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.8 years ago by ★ 6.5k • written 12.8 years ago by 53k
0
votes
2
replies
2.4k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.8 years ago love ▴ 150
0
votes
7
replies
2.9k
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 13.0 years ago by ★ 1.2k • written 13.0 years ago by ★ 2.0k
0
votes
9
replies
2.8k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 13.0 years ago by 53k • written 13.0 years ago by ★ 13k
0
votes
1
reply
1.7k
views
CQN normalization
cqn cqn
updated 13.4 years ago by ★ 6.5k • written 13.4 years ago by ▴ 90
0
votes
1
reply
1.5k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 13.4 years ago by ★ 6.5k • written 13.4 years ago by ★ 2.0k
0
votes
1
reply
1.6k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 13.5 years ago by ★ 6.5k • written 13.5 years ago by ▴ 30
0
votes
0
replies
1.2k
views
package announcement: cqn
Normalization cqn Normalization cqn
14.4 years ago Kasper Daniel Hansen ★ 6.5k
35 results • Page 1 of 1
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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