Showing : CQN • reset
2
votes
4
replies
1.2k
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 15 months ago by • 0
3
votes
12
replies
2.8k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.5 years ago by 43k • written 2.5 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
2.9 years ago Sally • 0
1
vote
1
reply
1.3k
views
CQN to DESeq2
cqn DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
votes
6
replies
1.9k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
4.4 years ago Saulius ▴ 10
0
votes
1
reply
1.1k
views
error using cqn package
Normalization cqn
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 30
0
votes
0
replies
1.0k
views
cqn vignette error
cqn normalization edger
5.9 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
951
views
CQN Normalization not removing bias
cqn
5.9 years ago nicholas.macknight • 0
0
votes
6
replies
3.0k
views
CQN to DEseq2
CQN deseq2
updated 2.9 years ago by • 0 • written 5.9 years ago by • 0
0
votes
1
reply
1.4k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
1.5k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 6.2 years ago by ★ 6.5k • written 6.2 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 6.4 years ago by 43k • written 6.4 years ago by • 0
1
vote
3
replies
1.7k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 6.6 years ago by ★ 6.5k • written 6.6 years ago by • 0
2
votes
2
replies
1.8k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
7.4 years ago shankasal • 0
6
votes
9
replies
7.1k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 7.4 years ago by ★ 29k • written 7.4 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 8.0 years ago by 43k • written 8.0 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 8.3 years ago by 43k • written 8.3 years ago by ▴ 10
0
votes
5
replies
4.7k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
9
votes
4
replies
4.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.6 years ago by 43k • written 8.6 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 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 20
0
votes
0
replies
1.4k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
9.7 years ago s1437643 ▴ 20
0
votes
9
replies
2.5k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 11.4 years ago by 43k • written 11.4 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 11.5 years ago by 25k • written 11.5 years ago by ▴ 380
0
votes
3
replies
2.3k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 11.9 years ago by 53k • written 11.9 years ago by ▴ 30
0
votes
1
reply
2.3k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.5 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 12.6 years ago by 53k • written 12.6 years ago by ▴ 90
0
votes
5
replies
3.8k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 12.6 years ago by 43k • written 12.6 years ago by ★ 13k
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.6 years ago by ★ 6.5k • written 12.6 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
12.7 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 12.9 years ago by ★ 1.2k • written 12.9 years ago by ★ 2.0k
0
votes
9
replies
2.7k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 12.9 years ago by 53k • written 12.9 years ago by ★ 13k
0
votes
1
reply
1.6k
views
CQN normalization
cqn cqn
updated 13.2 years ago by ★ 6.5k • written 13.2 years ago by ▴ 90
0
votes
1
reply
1.4k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 13.3 years ago by ★ 6.5k • written 13.3 years ago by ★ 2.0k
0
votes
1
reply
1.6k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 13.3 years ago by ★ 6.5k • written 13.3 years ago by ▴ 30
0
votes
0
replies
1.1k
views
package announcement: cqn
Normalization cqn Normalization cqn
14.2 years ago Kasper Daniel Hansen ★ 6.5k
35 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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