Showing : RUVSeq • reset
2
votes
2
replies
526
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
5 months ago BioinfGuru ▴ 70
0
votes
1
reply
549
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
0
replies
319
views
RUVg spike-in assumption global expression
RUVSeq RUVnormalize
6 months ago Erdi ▴ 10
0
votes
0
replies
305
views
determine k during RUVSeq
RUVSeq RUVnormalize
8 months ago Ειρήνη • 0
2
votes
9
replies
1.1k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 months ago by 67k • written 9 months ago by • 0
3
votes
6
replies
941
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
9 months ago nhaus ▴ 70
3
votes
2
replies
620
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 months ago Shaimaa Gamal • 0
4
votes
3
replies
779
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
2
votes
3
replies
724
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 0
2
votes
5
replies
882
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
12 months ago ctlong • 0
0
votes
6
replies
1.0k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 14 months ago by 43k • written 14 months ago by • 0
5
votes
9
replies
2.1k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 9 months ago by 52k • written 16 months ago by ▴ 10
3
votes
5
replies
1.6k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
0
votes
4
replies
1.0k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
17 months ago anne.hoffrichter • 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
1
vote
2
replies
1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
21 months ago AZ ▴ 30
0
votes
0
replies
574
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
21 months ago Luca • 0
1
vote
2
replies
1.4k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
22 months ago garbuzov • 0
3
votes
6
replies
1.4k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
24 months ago • updated 22 months ago Zainab ▴ 20
0
votes
1
reply
957
views
RUV with K more than 1.
RUVSeq
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by ▴ 10
0
votes
3
replies
1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
0
replies
656
views
RUVg for SNAP-ChIP ?
RUVSeq
2.1 years ago Bogdan ▴ 670
0
votes
1
reply
863
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.5 years ago Tongjun • 0
0
votes
4
replies
2.9k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.6 years ago Mohamed ▴ 30
1
vote
7
replies
2.0k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 50
1
vote
1
reply
942
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.7 years ago by 67k • written 2.7 years ago by ▴ 20
2
votes
7
replies
2.0k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.7 years ago Jess • 0
0
votes
5
replies
4.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.0 years ago by ★ 4.6k • written 3.8 years ago by • 0
1
vote
1
reply
1.0k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.3 years ago • updated 3.2 years ago Mallory ▴ 10
1
vote
5
replies
2.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 5 months ago by ▴ 70 • written 3.6 years ago by ▴ 50
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.6 years ago reganhayward • 0
2
votes
2
replies
1.7k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.7 years ago elizabethe819 • 0
0
votes
0
replies
796
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.8 years ago bioinfc • 0
0
votes
7
replies
2.0k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.9 years ago by ▴ 980 • written 4.0 years ago by • 0
5
votes
6
replies
2.0k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.3 years ago by 67k • written 4.3 years ago by ▴ 20
0
votes
2
replies
1.6k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
votes
0
replies
792
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.7 years ago acquaviva.massimo • 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.7 years ago by 52k • written 4.7 years ago by • 0
2
votes
4
replies
2.3k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
0
votes
3
replies
1.2k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.0 years ago by 67k • written 5.0 years ago by • 0
1
vote
4
replies
2.6k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.2 years ago Arindam ▴ 80
0
votes
2
replies
1.9k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.3 years ago by ▴ 980 • written 5.3 years ago by • 0
1
vote
1
reply
1.6k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 30
0
votes
1
reply
884
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
0
replies
1.0k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.6 years ago garbuzov • 0
0
votes
2
replies
2.9k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.6 years ago by ▴ 980 • written 5.8 years ago by • 0
2
votes
4
replies
2.7k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.7 years ago by ▴ 980 • written 5.7 years ago by ▴ 260
0
votes
0
replies
987
views
RUVseq: Use of known controls with RUVg
RUVseq
5.7 years ago bio.erikson • 0
1
vote
3
replies
2.6k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 660
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs by Gordon Smyth 52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Votes
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
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Bob ▴ 10
Popular Question to shepherl 4.1k
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 48 minutes ago
The city by the bay, 1 hour ago
Ukraine, 1 hour ago
USA, 1 hour ago
United States, 1 hour ago
Traffic: 573 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6