Showing : ruvseq • reset
2
votes
2
replies
514
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
4 months ago BioinfGuru ▴ 70
0
votes
1
reply
512
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
0
replies
303
views
RUVg spike-in assumption global expression
RUVSeq RUVnormalize
5 months ago Erdi ▴ 10
0
votes
0
replies
292
views
determine k during RUVSeq
RUVSeq RUVnormalize
7 months ago Ειρήνη • 0
2
votes
9
replies
1.0k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 months ago by 67k • written 8 months ago by • 0
3
votes
6
replies
905
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 months ago nhaus ▴ 70
3
votes
2
replies
605
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 months ago Shaimaa Gamal • 0
4
votes
3
replies
756
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
2
votes
3
replies
704
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 months ago by 67k • written 10 months ago by • 0
2
votes
5
replies
842
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
11 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 13 months ago by 43k • written 14 months ago by • 0
5
votes
9
replies
2.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 months ago by 52k • written 15 months ago by ▴ 10
3
votes
5
replies
1.5k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
votes
4
replies
985
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 20 months ago by 43k • written 20 months ago by ▴ 10
1
vote
2
replies
1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
20 months ago AZ ▴ 30
0
votes
0
replies
565
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
21 months ago garbuzov • 0
3
votes
6
replies
1.4k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
23 months ago • updated 21 months ago Zainab ▴ 20
0
votes
1
reply
947
views
RUV with K more than 1.
RUVSeq
updated 23 months ago by ★ 4.6k • written 23 months ago by ▴ 10
0
votes
3
replies
1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
votes
0
replies
646
views
RUVg for SNAP-ChIP ?
RUVSeq
2.1 years ago Bogdan ▴ 670
0
votes
1
reply
854
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.5 years ago Tongjun • 0
0
votes
4
replies
2.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.5 years ago Mohamed ▴ 30
1
vote
7
replies
2.0k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.5 years ago by 43k • written 2.6 years ago by ▴ 50
1
vote
1
reply
936
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 20
2
votes
7
replies
2.0k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.6 years ago Jess • 0
0
votes
5
replies
4.7k
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
3.2 years ago Mallory ▴ 10
1
vote
5
replies
2.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 4 months ago by ▴ 70 • written 3.5 years ago by ▴ 50
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.5 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
789
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 3.9 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 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
0
replies
783
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.6 years ago acquaviva.massimo • 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.6 years ago by 52k • written 4.6 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 4.9 years ago by 67k • written 4.9 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
5.1 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 5.2 years ago by ▴ 980 • written 5.2 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 30
0
votes
1
reply
877
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.5 years ago by 43k • written 5.5 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
2.8k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.6 years ago by ▴ 980 • written 5.7 years ago by • 0
2
votes
4
replies
2.7k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.6 years ago by ▴ 980 • written 5.6 years ago by ▴ 260
0
votes
0
replies
975
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
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to rohitsatyam102 ▴ 20
Popular Question to Hervé Pagès 16k
Teacher to dsull ▴ 40
Locations • All
United Kingdom, 11 minutes ago
University of Cambridge, UK | NIH Bethesda, MD, 40 minutes ago
United States, 1 hour ago
Sweden, 1 hour ago
India, 1 hour ago
Traffic: 662 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