Showing : CQN • reset
2
votes
4
replies
766
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 6 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 21 months ago by 43k • written 21 months ago by ▴ 10
0
votes
2
replies
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
2.2 years ago Sally • 0
1
vote
1
reply
1.1k
views
CQN to DESeq2
cqn DESeq2
updated 2.5 years ago by 43k • written 2.5 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
3.7 years ago Saulius ▴ 10
0
votes
1
reply
953
views
error using cqn package
Normalization cqn
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 30
0
votes
0
replies
884
views
cqn vignette error
cqn normalization edger
5.1 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
805
views
CQN Normalization not removing bias
cqn
5.2 years ago nicholas.macknight • 0
0
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6
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2.6k
views
CQN to DEseq2
CQN deseq2
updated 2.1 years ago by • 0 • written 5.2 years ago by • 0
0
votes
1
reply
1.2k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
votes
1
reply
1.3k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 5.5 years ago by ★ 6.5k • written 5.5 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 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
3
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1.5k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 5.9 years ago by ★ 6.5k • written 5.9 years ago by • 0
2
votes
2
replies
1.5k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.7 years ago shankasal • 0
6
votes
9
replies
6.0k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
4
votes
2
replies
1.5k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2 cqn normalization normalized counts
updated 7.3 years ago by 43k • written 7.3 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 7.6 years ago by 43k • written 7.6 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 7.7 years ago by 43k • written 7.7 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 7.9 years ago by 43k • written 7.9 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 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
0
votes
0
replies
1.2k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
9.0 years ago s1437643 ▴ 20
0
votes
9
replies
2.3k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.7 years ago by 43k • written 10.7 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 10.8 years ago by 25k • written 10.8 years ago by ▴ 380
0
votes
3
replies
2.1k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 11.2 years ago by 52k • written 11.2 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
11.8 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
1
reply
2.8k
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 11.9 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 11.9 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 11.9 years ago by ★ 6.5k • written 11.9 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 12.2 years ago by 52k • written 12.2 years ago by ★ 13k
0
votes
1
reply
1.5k
views
CQN normalization
cqn cqn
updated 12.5 years ago by ★ 6.5k • written 12.5 years ago by ▴ 90
0
votes
1
reply
1.3k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 12.6 years ago by ★ 6.5k • written 12.6 years ago by ★ 2.0k
0
votes
1
reply
1.5k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 12.6 years ago by ★ 6.5k • written 12.6 years ago by ▴ 30
0
votes
0
replies
1.0k
views
package announcement: cqn
Normalization cqn Normalization cqn
13.5 years ago Kasper Daniel Hansen ★ 6.5k
35 results • Page 1 of 1
Recent ...
Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
Answer: affymetrix by James W. MacDonald 67k
When posting it helps to think about the people you are asking for help. Your post is hidden within the dummy text that comes up when you i…
Answer: Problems with GSEA by Guido Hooiveld ★ 4.1k
The error `Duplicate values in names(stats) not allowed` (from `fgsea` that is used under the hood) shows that the input is not unique; in …
Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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Popular Question to Gordon Smyth 52k
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