Showing : cqn • reset
2
votes
4
replies
719
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 5 months ago by • 0
3
votes
12
replies
2.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
0
votes
2
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1.1k
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
2.1 years ago Sally • 0
1
vote
1
reply
1.1k
views
CQN to DESeq2
cqn DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
2
votes
6
replies
1.6k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.6 years ago Saulius ▴ 10
0
votes
1
reply
927
views
error using cqn package
Normalization cqn
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 30
0
votes
0
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874
views
cqn vignette error
cqn normalization edger
5.0 years ago Jenny Drnevich ★ 2.0k
0
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0
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793
views
CQN Normalization not removing bias
cqn
5.1 years ago nicholas.macknight • 0
0
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6
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2.5k
views
CQN to DEseq2
CQN deseq2
updated 2.1 years ago by • 0 • written 5.1 years ago by • 0
0
votes
1
reply
1.2k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
1
reply
1.3k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 5.4 years ago by ★ 6.5k • written 5.4 years ago by • 0
2
votes
1
reply
1.8k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
vote
3
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1.4k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 5.8 years ago by ★ 6.5k • written 5.8 years ago by • 0
2
votes
2
replies
1.5k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.6 years ago shankasal • 0
6
votes
9
replies
5.9k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
4
votes
2
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1.5k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2 cqn normalization normalized counts
updated 7.2 years ago by 43k • written 7.2 years ago by • 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 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
0
votes
5
replies
4.2k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 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 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
0
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0
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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
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2.3k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.6 years ago by 43k • written 10.6 years ago by ★ 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 10.7 years ago by 25k • written 10.7 years ago by ▴ 380
0
votes
3
replies
2.1k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 11.1 years ago by 52k • written 11.1 years ago by ▴ 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
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1
reply
2.7k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.8 years ago by 52k • written 11.8 years ago by ▴ 90
0
votes
5
replies
3.4k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 11.8 years ago by 43k • written 11.8 years ago by ★ 13k
0
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1
reply
1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.8 years ago by ★ 6.5k • written 11.8 years ago by 52k
0
votes
2
replies
2.1k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.9 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 12.1 years ago by ★ 1.2k • written 12.1 years ago by ★ 2.0k
0
votes
9
replies
2.3k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 12.1 years ago by 52k • written 12.1 years ago by ★ 13k
0
votes
1
reply
1.5k
views
CQN normalization
cqn cqn
updated 12.4 years ago by ★ 6.5k • written 12.4 years ago by ▴ 90
0
votes
1
reply
1.3k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 12.5 years ago by ★ 6.5k • written 12.5 years ago by ★ 2.0k
0
votes
1
reply
1.5k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 12.5 years ago by ★ 6.5k • written 12.5 years ago by ▴ 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: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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