Showing : cqn • reset
3
votes
12
replies
1.7k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 14 months ago by 42k • written 14 months ago by ▴ 10
0
votes
2
replies
850
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
19 months ago Sally • 0
1
vote
1
reply
919
views
CQN to DESeq2
cqn DESeq2
updated 23 months ago by 42k • written 23 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
3.1 years ago Saulius • 0
0
votes
1
reply
788
views
error using cqn package
Normalization cqn
updated 3.6 years ago by 66k • written 3.6 years ago by ▴ 30
0
votes
0
replies
740
views
cqn vignette error
cqn normalization edger
4.6 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
681
views
CQN Normalization not removing bias
cqn
4.6 years ago nicholas.macknight • 0
0
votes
6
replies
2.2k
views
CQN to DEseq2
CQN deseq2
updated 19 months ago by • 0 • written 4.6 years ago by • 0
0
votes
1
reply
994
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
votes
1
reply
1.1k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 5.0 years ago by ★ 6.5k • written 5.0 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 5.1 years ago by 42k • written 5.1 years ago by • 0
1
vote
3
replies
1.2k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 5.3 years ago by ★ 6.5k • written 5.3 years ago by • 0
2
votes
2
replies
1.3k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.1 years ago shankasal • 0
6
votes
9
replies
5.2k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.2 years ago by ★ 28k • written 6.2 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 6.7 years ago by 42k • written 6.7 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 7.0 years ago by 42k • written 7.0 years ago by ▴ 10
0
votes
5
replies
3.8k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 7.2 years ago by 42k • written 7.2 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 7.3 years ago by 42k • written 7.3 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 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 20
0
votes
0
replies
1.1k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
8.5 years ago s1437643 ▴ 20
0
votes
9
replies
2.1k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.2 years ago by 42k • written 10.2 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 10.2 years ago by 25k • written 10.2 years ago by ▴ 370
0
votes
3
replies
1.9k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 10.6 years ago by 51k • written 10.6 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
11.3 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
1
reply
2.6k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.3 years ago by 51k • written 11.3 years ago by ▴ 90
0
votes
5
replies
3.2k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 11.3 years ago by 42k • written 11.3 years ago by ★ 13k
0
votes
1
reply
1.5k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.4 years ago by ★ 6.5k • written 11.4 years ago by 51k
0
votes
2
replies
1.9k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.4 years ago love ▴ 150
0
votes
7
replies
2.3k
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 11.6 years ago by ★ 1.2k • written 11.6 years ago by ★ 2.0k
0
votes
9
replies
2.1k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 11.6 years ago by 51k • written 11.6 years ago by ★ 13k
0
votes
1
reply
1.3k
views
CQN normalization
cqn cqn
updated 11.9 years ago by ★ 6.5k • written 12.0 years ago by ▴ 90
0
votes
1
reply
1.2k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 12.0 years ago by ★ 6.5k • written 12.0 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 12.0 years ago by ★ 6.5k • written 12.0 years ago by ▴ 30
0
votes
0
replies
935
views
package announcement: cqn
Normalization cqn Normalization cqn
13.0 years ago Kasper Daniel Hansen ★ 6.5k
34 results • Page 1 of 1
Recent ...
Replies
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types) by Michael Love 42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results by Michael Love 42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results by V_Vibes • 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results by V_Vibes • 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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