Showing : cqn • reset
2
votes
4
replies
883
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 8 months ago by • 0
3
votes
12
replies
2.3k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
0
votes
6
replies
2.7k
views
CQN to DEseq2
CQN deseq2
updated 2.3 years ago by • 0 • written 5.3 years ago by • 0
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
2.3 years ago Sally • 0
1
vote
1
reply
1.1k
views
CQN to DESeq2
cqn DESeq2
updated 2.6 years ago by 43k • written 2.7 years ago by • 0
2
votes
6
replies
1.7k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.9 years ago Saulius ▴ 10
0
votes
1
reply
1.0k
views
error using cqn package
Normalization cqn
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 30
0
votes
0
replies
919
views
cqn vignette error
cqn normalization edger
5.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
845
views
CQN Normalization not removing bias
cqn
5.3 years ago nicholas.macknight • 0
0
votes
1
reply
1.3k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
1.4k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 5.7 years ago by ★ 6.5k • written 5.7 years ago by • 0
2
votes
1
reply
1.9k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
3
replies
1.5k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 6.0 years ago by ★ 6.5k • written 6.0 years ago by • 0
2
votes
2
replies
1.6k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.9 years ago shankasal • 0
6
votes
9
replies
6.4k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.9 years ago by ★ 28k • written 6.9 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 7.4 years ago by 43k • written 7.4 years ago by • 0
1
vote
1
reply
1.5k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2 cqn
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
0
votes
5
replies
4.4k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
9
votes
4
replies
4.0k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 30
4
votes
2
replies
2.7k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 20
0
votes
0
replies
1.3k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
9.2 years ago s1437643 ▴ 20
0
votes
9
replies
2.3k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.9 years ago by 43k • written 10.9 years ago by ★ 13k
3
votes
4
replies
4.6k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 380
0
votes
3
replies
2.1k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 11.3 years ago by 52k • written 11.3 years ago by ▴ 30
0
votes
1
reply
2.2k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.0 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 12.0 years ago by 52k • written 12.0 years ago by ▴ 90
0
votes
5
replies
3.5k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 12.0 years ago by 43k • written 12.0 years ago by ★ 13k
0
votes
1
reply
1.7k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 12.1 years ago by ★ 6.5k • written 12.1 years ago by 52k
0
votes
2
replies
2.2k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
12.1 years ago love ▴ 150
0
votes
7
replies
2.6k
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 12.3 years ago by ★ 1.2k • written 12.3 years ago by ★ 2.0k
0
votes
9
replies
2.5k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 12.3 years ago by 52k • written 12.3 years ago by ★ 13k
0
votes
1
reply
1.5k
views
CQN normalization
cqn cqn
updated 12.7 years ago by ★ 6.5k • written 12.7 years ago by ▴ 90
0
votes
1
reply
1.3k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 12.7 years ago by ★ 6.5k • written 12.7 years ago by ★ 2.0k
0
votes
1
reply
1.5k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 12.7 years ago by ★ 6.5k • written 12.7 years ago by ▴ 30
0
votes
0
replies
1.1k
views
package announcement: cqn
Normalization cqn Normalization cqn
13.7 years ago Kasper Daniel Hansen ★ 6.5k
35 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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