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 13 months ago by 42k • written 13 months ago by ▴ 10
0
votes
2
replies
805
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
18 months ago Sally • 0
1
vote
1
reply
886
views
CQN to DESeq2
cqn DESeq2
updated 21 months ago by 42k • written 22 months ago by • 0
2
votes
6
replies
1.3k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.0 years ago Saulius • 0
0
votes
1
reply
757
views
error using cqn package
Normalization cqn
updated 3.4 years ago by 65k • written 3.4 years ago by ▴ 30
0
votes
0
replies
721
views
cqn vignette error
cqn normalization edger
4.5 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
662
views
CQN Normalization not removing bias
cqn
4.5 years ago nicholas.macknight • 0
0
votes
6
replies
2.2k
views
CQN to DEseq2
CQN deseq2
updated 17 months ago by • 0 • written 4.5 years ago by • 0
0
votes
1
reply
960
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 4.8 years ago by ★ 6.5k • written 4.8 years ago by • 0
2
votes
1
reply
1.5k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
1
vote
3
replies
1.2k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 5.2 years ago by ★ 6.5k • written 5.2 years ago by • 0
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
6
votes
9
replies
5.0k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
4
votes
2
replies
1.3k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2 cqn normalization normalized counts
updated 6.6 years ago by 42k • written 6.6 years ago by • 0
1
vote
1
reply
1.3k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2 cqn
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 10
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 42k • written 7.0 years ago by ▴ 10
9
votes
4
replies
3.4k
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 42k • written 7.2 years ago by ▴ 30
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 ★ 28k • written 7.6 years ago by ▴ 20
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
9
replies
2.1k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.0 years ago by 42k • written 10.0 years ago by ★ 13k
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 25k • written 10.1 years ago by ▴ 360
0
votes
3
replies
1.9k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 10.5 years ago by 50k • written 10.5 years ago by ▴ 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
2.5k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.2 years ago by 50k • written 11.2 years ago by ▴ 90
0
votes
5
replies
3.2k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 11.2 years ago by 42k • written 11.2 years ago by ★ 13k
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 ★ 6.5k • written 11.2 years ago by 50k
0
votes
2
replies
1.8k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.3 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 11.5 years ago by ★ 1.2k • written 11.5 years ago by ★ 2.0k
0
votes
9
replies
2.0k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 11.5 years ago by 50k • written 11.5 years ago by ★ 13k
0
votes
1
reply
1.3k
views
CQN normalization
cqn cqn
updated 11.8 years ago by ★ 6.5k • written 11.8 years ago by ▴ 90
0
votes
1
reply
1.2k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 11.9 years ago by ★ 6.5k • written 11.9 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 11.9 years ago by ★ 6.5k • written 11.9 years ago by ▴ 30
0
votes
0
replies
918
views
package announcement: cqn
Normalization cqn Normalization cqn
12.8 years ago Kasper Daniel Hansen ★ 6.5k
34 results • Page 1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by jane • 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards • All
Popular Question to Hussain • 0
Popular Question to euge.eugenio ▴ 20
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Locations • All
Jerusalem, 1 minute ago
Vietnam, 8 minutes ago
130-C, DHA Phase 1, Karachi, 16 minutes ago
Greece, 16 minutes ago
Spain, 34 minutes ago
Traffic: 562 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6